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Romero JM, Serrano-Bueno G, Camacho-Fernández C, Vicente MH, Ruiz MT, Pérez-Castiñeira JR, Pérez-Hormaeche J, Nogueira FTS, Valverde F. CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits. THE PLANT CELL 2024; 36:2086-2102. [PMID: 38513610 PMCID: PMC11132886 DOI: 10.1093/plcell/koae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.
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Affiliation(s)
- Jose M Romero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Gloria Serrano-Bueno
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Carolina Camacho-Fernández
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
- Universidad Politécnica de Valencia, Vicerrectorado de Investigación, 46022 Valencia, Spain
| | - Mateus Henrique Vicente
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo (USP), Piracicaba, 13418-900 São Paulo, Brazil
| | - M Teresa Ruiz
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
| | - J Román Pérez-Castiñeira
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Javier Pérez-Hormaeche
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
| | - Fabio T S Nogueira
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo (USP), Piracicaba, 13418-900 São Paulo, Brazil
| | - Federico Valverde
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
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2
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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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3
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Bao H, Sun R, Iwano M, Yoshitake Y, Aki SS, Umeda M, Nishihama R, Yamaoka S, Kohchi T. Conserved CKI1-mediated signaling is required for female germline specification in Marchantia polymorpha. Curr Biol 2024; 34:1324-1332.e6. [PMID: 38295795 DOI: 10.1016/j.cub.2024.01.013] [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] [Received: 09/06/2023] [Revised: 12/08/2023] [Accepted: 01/05/2024] [Indexed: 03/28/2024]
Abstract
In land plants, gametes derive from a small number of dedicated haploid cells.1 In angiosperms, one central cell and one egg cell are differentiated in the embryo sac as female gametes for double fertilization, while in non-flowering plants, only one egg cell is generated in the female sexual organ, called the archegonium.2,3 The central cell specification of Arabidopsis thaliana is controlled by the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1), which is a two-component signaling (TCS) activator sharing downstream regulatory components with the cytokinin signaling pathway.4,5,6,7 Our phylogenetic analysis suggested that CKI1 orthologs broadly exist in land plants. However, the role of CKI1 in non-flowering plants remains unclear. Here, we found that the sole CKI1 ortholog in the liverwort Marchantia polymorpha, MpCKI1, which functions through conserved downstream TCS components, regulates the female germline specification for egg cell development in the archegonium. In M. polymorpha, the archegonium develops three-dimensionally from a single cell accumulating MpBONOBO (MpBNB), a master regulator for germline initiation and differentiation.8 We visualized female germline specification by capturing the distribution pattern of MpBNB in discrete stages of early archegonium development, and found that MpBNB accumulation is restricted to female germline cells. MpCKI1 is required for the proper MpBNB accumulation in the female germline, and is critical for the asymmetric cell divisions that specify the female germline cells. These results suggest that CKI1-mediated TCS originated during early land plant evolution and participates in female germ cell specification in deeply diverged plant lineages.
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Affiliation(s)
- Haonan Bao
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Rui Sun
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Megumi Iwano
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Shiori S Aki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Shohei Yamaoka
- 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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4
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Gutsche N, Koczula J, Trupp M, Holtmannspötter M, Appelfeller M, Rupp O, Busch A, Zachgo S. MpTGA, together with MpNPR, regulates sexual reproduction and independently affects oil body formation in Marchantia polymorpha. THE NEW PHYTOLOGIST 2024; 241:1559-1573. [PMID: 38095258 DOI: 10.1111/nph.19472] [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: 08/30/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
In angiosperms, basic leucine-zipper (bZIP) TGACG-motif-binding (TGA) transcription factors (TFs) regulate developmental and stress-related processes, the latter often involving NON EXPRESSOR OF PATHOGENESIS-RELATED GENES (NPR) coregulator interactions. To gain insight into their functions in an early diverging land-plant lineage, the single MpTGA and sole MpNPR genes were investigated in the liverwort Marchantia polymorpha. We generated Marchantia MpTGA and MpNPR knockout and overexpression mutants and conducted morphological, transcriptomic and expression studies. Furthermore, we investigated MpTGA interactions with wild-type and mutagenized MpNPR and expanded our analyses including TGA TFs from two streptophyte algae. Mptga mutants fail to induce the switch from vegetative to reproductive development and lack gametangiophore formation. MpTGA and MpNPR proteins interact and Mpnpr mutant analysis reveals a novel coregulatory NPR role in sexual reproduction. Additionally, MpTGA acts independently of MpNPR as a repressor of oil body (OB) formation and can thereby affect herbivory. The single MpTGA TF exerts a dual role in sexual reproduction and OB formation in Marchantia. Common activities of MpTGA/MpNPR in sexual development suggest that coregulatory interactions were established after emergence of land-plant-specific NPR genes and contributed to the diversification of TGA TF functions during land-plant evolution.
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Affiliation(s)
- Nora Gutsche
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Jens Koczula
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Melanie Trupp
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Michael Holtmannspötter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | | | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Andrea Busch
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Sabine Zachgo
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
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5
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Diao R, Zhao M, Liu Y, Zhang Z, Zhong B. The advantages of crosstalk during the evolution of the BZR1-ARF6-PIF4 (BAP) module. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2631-2644. [PMID: 37552560 DOI: 10.1111/jipb.13554] [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: 03/16/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023]
Abstract
The BAP module, comprising BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), functions as a molecular hub to orchestrate plant growth and development. In Arabidopsis thaliana, components of the BAP module physically interact to form a complex system that integrates light, brassinosteroid (BR), and auxin signals. Little is known about the origin and evolution of the BAP module. Here, we conducted comparative genomic and transcriptomic analyses to investigate the evolution and functional diversification of the BAP module. Our results suggest that the BAP module originated in land plants and that the ζ, ε, and γ whole-genome duplication/triplication events contributed to the expansion of BAP module components in seed plants. Comparative transcriptomic analysis suggested that the prototype BAP module arose in Marchantia polymorpha, experienced stepwise evolution, and became established as a mature regulatory system in seed plants. We developed a formula to calculate the signal transduction productivity of the BAP module and demonstrate that more crosstalk among components enables higher signal transduction efficiency. Our results reveal the evolutionary history of the BAP module and provide insights into the evolution of plant signaling networks and the strategies employed by plants to integrate environmental and endogenous signals.
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Affiliation(s)
- Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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6
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Saito M, Momiki R, Ebine K, Yoshitake Y, Nishihama R, Miyakawa T, Nakano T, Mitsuda N, Araki T, Kohchi T, Yamaoka S. A bHLH heterodimer regulates germ cell differentiation in land plant gametophytes. Curr Biol 2023; 33:4980-4987.e6. [PMID: 37776860 DOI: 10.1016/j.cub.2023.09.020] [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] [Received: 06/03/2023] [Revised: 08/20/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023]
Abstract
Land plants are a monophyletic group of photosynthetic eukaryotes that diverged from streptophyte algae about 470 million years ago. During both the alternating haploid and diploid stages of the life cycle, land plants form multicellular bodies.1,2,3,4 The haploid multicellular body (gametophyte) produces progenitor cells that give rise to gametes and the reproductive organs.5,6,7,8 In the liverwort Marchantia polymorpha, differentiation of the initial cells of gamete-producing organs (gametangia) from the gametophyte is regulated by MpBONOBO (MpBNB), a member of the basic helix-loop-helix (bHLH) transcription factor subfamily VIIIa. In Arabidopsis thaliana, specification of generative cells in developing male gametophytes (pollen) requires redundant action of BNB1 and BNB2.9 Subfamily XI bHLHs, such as LOTUS JAPONICUS ROOTHAIRLESS LIKE1 (LRL1)/DEFECTIVE REGION OF POLLEN1 (DROP1) and LRL2/DROP2 in A. thaliana and the single LRL/DROP protein MpLRL in M. polymorpha, are the evolutionarily conserved regulators of rooting system development.10 Although the role of LRL1/DROP1 and LRL2/DROP2 in gametogenesis remains unclear, their loss leads to the formation of abnormal pollen devoid of sperm cells.11 Here, we show that BNBs and LRL/DROPs co-localize to gametophytic cell nuclei and form heterodimers. LRL1/DROP1 and LRL2/DROP2 act redundantly to regulate BNB expression for generative cell specification in A. thaliana after asymmetric division of the haploid microspore. MpLRL is required for differentiation of MpBNB-expressing gametangium initial cells in M. polymorpha gametophytes. Our findings suggest that broadly expressed LRL/DROP stabilizes BNB expression, leading to the formation of an evolutionarily conserved bHLH heterodimer, which regulates germ cell differentiation in the haploid gametophyte of land plants.
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Affiliation(s)
- Misaki Saito
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryosuke Momiki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kazuo Ebine
- National Institute for Basic Biology (NIBB), Okazaki, Aichi 444-8585, Japan; The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | | | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Takuya Miyakawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takeshi Nakano
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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7
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Kanesaka Y, Inoue K, Tomita Y, Yamaoka S, Araki T. Circadian clock does not play an essential role in daylength measurement for growth-phase transition in Marchantia polymorpha. FRONTIERS IN PLANT SCIENCE 2023; 14:1275503. [PMID: 38023914 PMCID: PMC10673691 DOI: 10.3389/fpls.2023.1275503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Daylength is perceived as a seasonal cue to induce growth-phase transition at a proper time of a year. The core of the mechanism of daylength measurement in angiosperms lies in the circadian clock-controlled expression of regulators of growth-phase transition. However, the roles of the circadian clock in daylength measurement in basal land plants remain largely unknown. In this study, we investigated the contribution of circadian clock to daylength measurement in a basal land plant, the liverwort Marchantia polymorpha. In M. polymorpha, transition from vegetative to reproductive phase under long-day conditions results in differentiation of sexual branches called gametangiophores which harbor gametangia. First, we showed that a widely used wild-type accession Takaragaike-1 is an obligate long-day plant with a critical daylength of about 10 hours and requires multiple long days. Then, we compared the timing of gametangiophore formation between wild type and circadian clock mutants in long-day and short-day conditions. Mutations in two clock genes, MpTIMING OF CAB EXPRESSION 1 and MpPSEUDO-RESPONSE REGULATOR, had no significant effects on the timing of gametangiophore formation. In addition, when M. polymorpha plants were treated with a chemical which lengthens circadian period, there was no significant effect on the timing of gametangiophore formation, either. We next observed the timing of gametangiophore formation under various non-24-h light/dark cycles to examine the effect of phase alteration in circadian rhythms. The results suggest that daylength measurement in M. polymorpha is based on the relative amount of light and darkness within a cycle rather than the intrinsic rhythms generated by circadian clock. Our findings suggest that M. polymorpha has a daylength measurement system which is different from that of angiosperms centered on the circadian clock function.
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Affiliation(s)
- Yuki Kanesaka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yuki Tomita
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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8
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Pietrykowska H, Alisha A, Aggarwal B, Watanabe Y, Ohtani M, Jarmolowski A, Sierocka I, Szweykowska-Kulinska Z. Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development. PLANT MOLECULAR BIOLOGY 2023; 113:121-142. [PMID: 37991688 PMCID: PMC10721683 DOI: 10.1007/s11103-023-01392-y] [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: 06/27/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023]
Abstract
A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.
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Affiliation(s)
- Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Alisha Alisha
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Chiba, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Kanagawa, Japan
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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9
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Yadav A. How gibberellin-related compounds shape far-red light responses in Marchantia polymorpha. THE PLANT CELL 2023; 35:3922-3923. [PMID: 37594120 PMCID: PMC10615204 DOI: 10.1093/plcell/koad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/19/2023]
Affiliation(s)
- Arpita Yadav
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Biology Department, University of Massachusetts Amherst, MA 01003, USA
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10
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Sun R, Okabe M, Miyazaki S, Ishida T, Mashiguchi K, Inoue K, Yoshitake Y, Yamaoka S, Nishihama R, Kawaide H, Nakajima M, Yamaguchi S, Kohchi T. Biosynthesis of gibberellin-related compounds modulates far-red light responses in the liverwort Marchantia polymorpha. THE PLANT CELL 2023; 35:4111-4132. [PMID: 37597168 PMCID: PMC10615216 DOI: 10.1093/plcell/koad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/21/2023]
Abstract
Gibberellins (GAs) are key phytohormones that regulate growth, development, and environmental responses in angiosperms. From an evolutionary perspective, all major steps of GA biosynthesis are conserved among vascular plants, while GA biosynthesis intermediates such as ent-kaurenoic acid (KA) are also produced by bryophytes. Here, we show that in the liverwort Marchantia polymorpha, KA and GA12 are synthesized by evolutionarily conserved enzymes, which are required for developmental responses to far-red light (FR). Under FR-enriched conditions, mutants of various biosynthesis enzymes consistently exhibited altered thallus growth allometry, delayed initiation of gametogenesis, and abnormal morphology of gamete-bearing structures (gametangiophores). By chemical treatments and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses, we confirmed that these phenotypes were caused by the deficiency of some GA-related compounds derived from KA, but not bioactive GAs from vascular plants. Transcriptome analysis showed that FR enrichment induced the up-regulation of genes related to stress responses and secondary metabolism in M. polymorpha, which was largely dependent on the biosynthesis of GA-related compounds. Due to the lack of canonical GA receptors in bryophytes, we hypothesize that GA-related compounds are commonly synthesized in land plants but were co-opted independently to regulate responses to light quality change in different plant lineages during the past 450 million years of evolution.
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Affiliation(s)
- Rui Sun
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | - Maiko Okabe
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | - Sho Miyazaki
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, 183-8509,Japan
| | - Toshiaki Ishida
- Institute for Chemical Research, Kyoto University, Uji 611-0011,Japan
| | | | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda 278-8510,Japan
| | - Hiroshi Kawaide
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509,Japan
| | - Masatoshi Nakajima
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo 113-8657,Japan
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502,Japan
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11
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Gururani MA. Photobiotechnology for abiotic stress resilient crops: Recent advances and prospects. Heliyon 2023; 9:e20158. [PMID: 37810087 PMCID: PMC10559926 DOI: 10.1016/j.heliyon.2023.e20158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Massive crop failures worldwide are caused by abiotic stress. In plants, adverse environmental conditions cause extensive damage to the overall physiology and agronomic yield at various levels. Phytochromes are photosensory phosphoproteins that absorb red (R)/far red (FR) light and play critical roles in different physiological and biochemical responses to light. Considering the role of phytochrome in essential plant developmental processes, genetically manipulating its expression offers a promising approach to crop improvement. Through modulated phytochrome-mediated signalling pathways, plants can become more resistant to environmental stresses by increasing photosynthetic efficiency, antioxidant activity, and expression of genes associated with stress resistance. Plant growth and development in adverse environments can be improved by understanding the roles of phytochromes in stress tolerance characteristics. A comprehensive overview of recent findings regarding the role of phytochromes in modulating abiotic stress by discussing biochemical and molecular aspects of these mechanisms of photoreceptors is offered in this review.
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Affiliation(s)
- Mayank Anand Gururani
- Biology Department, College of Science, UAE University, Al Ain, United Arab Emirates
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12
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Cui Y, Hisanaga T, Kajiwara T, Yamaoka S, Kohchi T, Goh T, Nakajima K. Three-Dimensional Morphological Analysis Revealed the Cell Patterning Bases for the Sexual Dimorphism Development in the Liverwort Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2023; 64:866-879. [PMID: 37225421 DOI: 10.1093/pcp/pcad048] [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: 01/24/2023] [Revised: 04/21/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023]
Abstract
In land plants, sexual dimorphism can develop in both diploid sporophytes and haploid gametophytes. While developmental processes of sexual dimorphism have been extensively studied in the sporophytic reproductive organs of model flowering plants such as stamens and carpels of Arabidopsis thaliana, those occurring in gametophyte generation are less well characterized due to the lack of amenable model systems. In this study, we performed three-dimensional morphological analyses of gametophytic sexual branch differentiation in the liverwort Marchantia polymorpha, using high-depth confocal imaging and a computational cell segmentation technique. Our analysis revealed that the specification of germline precursors initiates in a very early stage of sexual branch development, where incipient branch primordia are barely recognizable in the apical notch region. Moreover, spatial distribution patterns of germline precursors differ between males and females from the initial stage of primordium development in a manner dependent on the master sexual differentiation regulator MpFGMYB. At later stages, distribution patterns of germline precursors predict the sex-specific gametangia arrangement and receptacle morphologies seen in mature sexual branches. Taken together, our data suggest a tightly coupled progression of germline segregation and sexual dimorphism development in M. polymorpha.
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Affiliation(s)
- Yihui Cui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
| | - Tetsuya Hisanaga
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tomoaki Kajiwara
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502 Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502 Japan
| | - Tatsuaki Goh
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
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13
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Lee N, Ozaki Y, Hempton AK, Takagi H, Purusuwashi S, Song YH, Endo M, Kubota A, Imaizumi T. The FLOWERING LOCUS T gene expression is controlled by high-irradiance response and external coincidence mechanism in long days in Arabidopsis. THE NEW PHYTOLOGIST 2023; 239:208-221. [PMID: 37084001 PMCID: PMC10244125 DOI: 10.1111/nph.18932] [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: 01/06/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
In natural long days, the florigen gene FLOWERING LOCUS T (FT) shows a bimodal expression pattern with morning and dusk peaks in Arabidopsis. This pattern differs from the one observed in the laboratory, and little is known about underlying mechanisms. A red : far-red (R : FR) ratio difference between sunlight and fluorescent light causes this FT pattern mismatch. We showed that bimodal FT expression patterns were induced in a day longer than 14 h with sunlight R : FR (= c. 1) conditions. By circadian gating experiments, we found that cumulative exposure of R : FR-adjusted light (R : FR ratio was adjusted to 1 with FR supplement) spanning from the afternoon to the next morning required full induction of FT in the morning. Conversely, only 2 h of R : FR adjustment in the late afternoon was sufficient for FT induction at dusk. We identified that phytochrome A (phyA) is required for the morning FT expression in response to the R : FR adjustment on the previous day. As a part of this mechanism, we showed that PHYTOCHROME-INTERACTING FACTOR 7 contributes to FT regulation. Our results suggest that phyA-mediated high-irradiance response and the external coincidence mechanism contribute to morning FT induction under natural long-day conditions.
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Affiliation(s)
- Nayoung Lee
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Yusuke Ozaki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Andrew K. Hempton
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Hiroshi Takagi
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Savita Purusuwashi
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Young Hun Song
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Motomu Endo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Akane Kubota
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8602, Japan
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14
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Sharma A, Samtani H, Sahu K, Sharma AK, Khurana JP, Khurana P. Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review. Int J Biol Macromol 2023:125234. [PMID: 37290549 DOI: 10.1016/j.ijbiomac.2023.125234] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.
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Affiliation(s)
- Aishwarye Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Karishma Sahu
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Jitendra Paul Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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15
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Fisher TJ, Flores-Sandoval E, Alvarez JP, Bowman JL. PIN-FORMED is required for shoot phototropism/gravitropism and facilitates meristem formation in Marchantia polymorpha. THE NEW PHYTOLOGIST 2023; 238:1498-1515. [PMID: 36880411 DOI: 10.1111/nph.18854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
PIN-FORMED auxin efflux transporters, a subclass of which is plasma membrane-localised, mediate a variety of land-plant developmental processes via their polar localisation and subsequent directional auxin transport. We provide the first characterisation of PIN proteins in liverworts using Marchantia polymorpha as a model system. Marchantia polymorpha possesses a single PIN-FORMED gene, whose protein product is predicted to be plasma membrane-localised, MpPIN1. To characterise MpPIN1, we created loss-of-function alleles and produced complementation lines in both M. polymorpha and Arabidopsis. In M. polymorpha, gene expression and protein localisation were tracked using an MpPIN1 transgene encoding a translationally fused fluorescent protein. Overexpression of MpPIN1 can partially complement loss of an orthologous gene, PIN-FORMED1, in Arabidopsis. In M. polymorpha, MpPIN1 influences development in numerous ways throughout its life cycle. Most notably, MpPIN1 is required to establish gemmaling dorsiventral polarity and for orthotropic growth of gametangiophore stalks, where MpPIN1 is basally polarised. PIN activity is largely conserved within land plants, with PIN-mediated auxin flow providing a flexible mechanism to organise growth. Specifically, PIN is fundamentally linked to orthotropism and to the establishment of de novo meristems, the latter potentially involving the formation of both auxin biosynthesis maxima and auxin-signalling minima.
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Affiliation(s)
- Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Vic., 3800, Australia
| | - Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Vic., 3800, Australia
| | - John P Alvarez
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Vic., 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, Vic., 3800, Australia
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16
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Liang Y, Heyman J, Lu R, De Veylder L. Evolution of wound-activated regeneration pathways in the plant kingdom. Eur J Cell Biol 2023; 102:151291. [PMID: 36709604 DOI: 10.1016/j.ejcb.2023.151291] [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: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Regeneration serves as a self-protective mechanism that allows a tissue or organ to recover its entire form and function after suffering damage. However, the regenerative capacity varies greatly within the plant kingdom. Primitive plants frequently display an amazing regenerative ability as they have developed a complex system and strategy for long-term survival under extreme stress conditions. The regenerative ability of dicot species is highly variable, but that of monocots often exhibits extreme recalcitrance to tissue replenishment. Recent studies have revealed key factors and signals that affect cell fate during plant regeneration, some of which are conserved among the plant lineage. Among these, several members of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors have been implicated in wound signaling, playing crucial roles in the regenerative mechanisms after different types of wounding. An understanding of plant regeneration may ultimately lead to an increased regenerative potential of recalcitrant species, producing more high-yielding, multi-resistant and environmentally friendly crops and ensuring the long-term development of global agriculture.
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Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
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17
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Bowman JL, Arteaga-Vazquez M, Berger F, Briginshaw LN, Carella P, Aguilar-Cruz A, Davies KM, Dierschke T, Dolan L, Dorantes-Acosta AE, Fisher TJ, Flores-Sandoval E, Futagami K, Ishizaki K, Jibran R, Kanazawa T, Kato H, Kohchi T, Levins J, Lin SS, Nakagami H, Nishihama R, Romani F, Schornack S, Tanizawa Y, Tsuzuki M, Ueda T, Watanabe Y, Yamato KT, Zachgo S. The renaissance and enlightenment of Marchantia as a model system. THE PLANT CELL 2022; 34:3512-3542. [PMID: 35976122 PMCID: PMC9516144 DOI: 10.1093/plcell/koac219] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 05/07/2023]
Abstract
The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.
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Affiliation(s)
| | - Mario Arteaga-Vazquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Frederic Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Liam N Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Philip Carella
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adolfo Aguilar-Cruz
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4442, New Zealand
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Liam Dolan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Ana E Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Kazutaka Futagami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | | | - Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Auckland 1142, New Zealand
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Jonathan Levins
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Sabine Zachgo
- Division of Botany, School of Biology and Chemistry, Osnabrück University, Osnabrück 49076, Germany
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18
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Goto-Yamada S, Oikawa K, Yamato KT, Kanai M, Hikino K, Nishimura M, Mano S. Image-Based Analysis Revealing the Molecular Mechanism of Peroxisome Dynamics in Plants. Front Cell Dev Biol 2022; 10:883491. [PMID: 35592252 PMCID: PMC9110829 DOI: 10.3389/fcell.2022.883491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are present in eukaryotic cells and have essential roles in various biological processes. Plant peroxisomes proliferate by de novo biosynthesis or division of pre-existing peroxisomes, degrade, or replace metabolic enzymes, in response to developmental stages, environmental changes, or external stimuli. Defects of peroxisome functions and biogenesis alter a variety of biological processes and cause aberrant plant growth. Traditionally, peroxisomal function-based screening has been employed to isolate Arabidopsis thaliana mutants that are defective in peroxisomal metabolism, such as lipid degradation and photorespiration. These analyses have revealed that the number, subcellular localization, and activity of peroxisomes are closely related to their efficient function, and the molecular mechanisms underlying peroxisome dynamics including organelle biogenesis, protein transport, and organelle interactions must be understood. Various approaches have been adopted to identify factors involved in peroxisome dynamics. With the development of imaging techniques and fluorescent proteins, peroxisome research has been accelerated. Image-based analyses provide intriguing results concerning the movement, morphology, and number of peroxisomes that were hard to obtain by other approaches. This review addresses image-based analysis of peroxisome dynamics in plants, especially A. thaliana and Marchantia polymorpha.
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Affiliation(s)
- Shino Goto-Yamada
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazusato Oikawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Katsuyuki T. Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Kazumi Hikino
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Mikio Nishimura
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
- *Correspondence: Shoji Mano
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19
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Briginshaw LN, Flores‐Sandoval E, Dierschke T, Alvarez JP, Bowman JL. KANADI promotes thallus differentiation and FR-induced gametangiophore formation in the liverwort Marchantia. THE NEW PHYTOLOGIST 2022; 234:1377-1393. [PMID: 35181887 PMCID: PMC9311212 DOI: 10.1111/nph.18046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/07/2022] [Indexed: 05/26/2023]
Abstract
In angiosperms, KANADI transcription factors have roles in the sporophyte generation regulating tissue polarity, organogenesis and shade avoidance responses, but are not required during the gametophyte generation. Whether these roles are conserved in the gametophyte-dominant bryophyte lineages is unknown, which we examined by characterising the sole KANADI ortholog, MpKAN, in the liverwort Marchantia polymorpha. In contrast to angiosperm orthologs, MpKAN functions in the gametophyte generation in Marchantia, where it regulates apical branching and tissue differentiation, but does not influence tissue polarity in either generation. MpKAN can partially rescue the sporophyte polarity defects of kanadi mutants in Arabidopsis, indicating that MpKAN has conserved biochemical activity to its angiosperm counterparts. Mpkan loss-of-function plants display defects in far-red (FR) light responses. Mpkan plants have reduced FR-induced growth tropisms, have a delayed transition to sexual reproduction and fail to correctly form gametangiophores. Our results indicate that MpKAN is a modulator of FR responses, which may reflect a conserved role for KANADI across land plants. Under FR, MpKAN negatively regulates MpDELLA expression, suggesting that MpKAN and MpDELLA act in a pathway regulating FR responses, placing MpKAN in a gene regulatory network exhibiting similarities with those of angiosperms.
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Affiliation(s)
- Liam N. Briginshaw
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
| | - Eduardo Flores‐Sandoval
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
| | - Tom Dierschke
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
| | - John P. Alvarez
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
| | - John L. Bowman
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
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20
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Abstract
The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.
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21
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Soriano G, Kneeshaw S, Jimenez-Aleman G, Zamarreño ÁM, Franco-Zorrilla JM, Rey-Stolle MF, Barbas C, García-Mina JM, Solano R. An evolutionarily ancient fatty acid desaturase is required for the synthesis of hexadecatrienoic acid, which is the main source of the bioactive jasmonate in Marchantia polymorpha. THE NEW PHYTOLOGIST 2022; 233:1401-1413. [PMID: 34846752 DOI: 10.1111/nph.17850] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Jasmonates are fatty acid-derived hormones that regulate multiple aspects of plant development, growth and stress responses. Bioactive jasmonates, defined as the ligands of the conserved COI1 receptor, differ between vascular plants and bryophytes (jasmonoyl-l-isoleucine (JA-Ile) and dinor-12-oxo-10,15(Z)-phytodienoic acid (dn-OPDA), respectively). The biosynthetic pathways of JA-Ile in the model vascular plant Arabidopsis thaliana have been elucidated. However, the details of dn-OPDA biosynthesis in bryophytes are still unclear. Here, we identify an orthologue of Arabidopsis fatty-acid-desaturase 5 (AtFAD5) in the model liverwort Marchantia polymorpha and show that FAD5 function is ancient and conserved between species separated by more than 450 million years (Myr) of independent evolution. Similar to AtFAD5, MpFAD5 is required for the synthesis of 7Z-hexadecenoic acid. Consequently, in Mpfad5 mutants, the hexadecanoid pathway is blocked, dn-OPDA concentrations are almost completely depleted and normal chloroplast development is impaired. Our results demonstrate that the main source of wounding-induced dn-OPDA in Marchantia is the hexadecanoid pathway and the contribution of the octadecanoid pathway (i.e. from OPDA) is minimal. Remarkably, despite extremely low concentrations of dn-OPDA, MpCOI1-mediated responses to wounding and insect feeding can still be activated in Mpfad5, suggesting that dn-OPDA may not be the only bioactive jasmonate and COI1 ligand in Marchantia.
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Affiliation(s)
- Gonzalo Soriano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
- Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios 53, Logroño (La Rioja), 26006, Spain
| | - Sophie Kneeshaw
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
| | - Guillermo Jimenez-Aleman
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
| | - Ángel M Zamarreño
- Department of Environmental Biology, University of Navarra, Navarra, 31008, Spain
| | - José Manuel Franco-Zorrilla
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
| | - Mª Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, 28668, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, 28668, Spain
| | - Jose M García-Mina
- Department of Environmental Biology, University of Navarra, Navarra, 31008, Spain
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
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22
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Yamaoka S, Inoue K, Araki T. Regulation of gametangia and gametangiophore initiation in the liverwort Marchantia polymorpha. PLANT REPRODUCTION 2021; 34:297-306. [PMID: 34117568 DOI: 10.1007/s00497-021-00419-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
The liverwort Marchantia polymorpha regulates gametangia and gametangiophore development by using evolutionarily conserved regulatory modules that are shared with angiosperm mechanisms regulating flowering and germ cell differentiation. Bryophytes, the earliest diverged lineage of land plants comprised of liverworts, mosses, and hornworts, produce gametes in gametangia, reproductive organs evolutionarily conserved but lost in extant angiosperms. Initiation of gametangium development is dependent on environmental factors such as light, although the underlying mechanisms remain elusive. Recent studies showed that the liverwort Marchantia polymorpha regulates development of gametangia and stalked receptacles called gametangiophores by using conserved regulatory modules which, in angiosperms, are involved in light signaling, microRNA-mediated flowering regulation, and germ cell differentiation. These findings suggest that these modules were acquired by a common ancestor of land plants before divergence of bryophytes, and were later recruited to flowering mechanism in angiosperms.
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Affiliation(s)
- Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
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23
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Dierschke T, Flores-Sandoval E, Rast-Somssich MI, Althoff F, Zachgo S, Bowman JL. Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha. eLife 2021; 10:57088. [PMID: 34533136 PMCID: PMC8476127 DOI: 10.7554/elife.57088] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/15/2021] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic life cycles alternate between haploid and diploid phases and in phylogenetically diverse unicellular eukaryotes, expression of paralogous homeodomain genes in gametes primes the haploid-to-diploid transition. In the unicellular chlorophyte alga Chlamydomonas, KNOX and BELL TALE-homeodomain genes mediate this transition. We demonstrate that in the liverwort Marchantia polymorpha, paternal (sperm) expression of three of five phylogenetically diverse BELL genes, MpBELL234, and maternal (egg) expression of both MpKNOX1 and MpBELL34 mediate the haploid-to-diploid transition. Loss-of-function alleles of MpKNOX1 result in zygotic arrest, whereas a loss of either maternal or paternal MpBELL234 results in variable zygotic and early embryonic arrest. Expression of MpKNOX1 and MpBELL34 during diploid sporophyte development is consistent with a later role for these genes in patterning the sporophyte. These results indicate that the ancestral mechanism to activate diploid gene expression was retained in early diverging land plants and subsequently co-opted during evolution of the diploid sporophyte body.
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Affiliation(s)
- Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, Australia.,Botany Department, University of Osnabrück, Osnabrück, Germany
| | | | | | - Felix Althoff
- Botany Department, University of Osnabrück, Osnabrück, Germany
| | - Sabine Zachgo
- Botany Department, University of Osnabrück, Osnabrück, Germany
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Australia
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24
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Hernández-García J, Sun R, Serrano-Mislata A, Inoue K, Vargas-Chávez C, Esteve-Bruna D, Arbona V, Yamaoka S, Nishihama R, Kohchi T, Blázquez MA. Coordination between growth and stress responses by DELLA in the liverwort Marchantia polymorpha. Curr Biol 2021; 31:3678-3686.e11. [PMID: 34214451 DOI: 10.1016/j.cub.2021.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/27/2021] [Accepted: 06/03/2021] [Indexed: 12/19/2022]
Abstract
Plant survival depends on the optimal use of resources under variable environmental conditions. Among the mechanisms that mediate the balance between growth, differentiation, and stress responses, the regulation of transcriptional activity by DELLA proteins stands out. In angiosperms, DELLA accumulation promotes defense against biotic and abiotic stress and represses cell division and expansion, while the loss of DELLA function is associated with increased plant size and sensitivity toward stress.1 Given that DELLA protein stability is dependent on gibberellin (GA) levels2 and GA metabolism is influenced by the environment,3 this pathway is proposed to relay environmental information to the transcriptional programs that regulate growth and stress responses in angiosperms.4,5 However, DELLA genes are also found in bryophytes, whereas canonical GA receptors have been identified only in vascular plants.6-10 Thus, it is not clear whether these regulatory functions of DELLA predated or emerged with typical GA signaling. Here, we show that, as in vascular plants, the only DELLA in the liverwort Marchantia polymorpha also participates in the regulation of growth and key developmental processes and promotes oxidative stress tolerance. Moreover, part of these effects is likely caused by the conserved physical interaction with the MpPIF transcription factor. Therefore, we suggest that the role in the coordination of growth and stress responses was already encoded in the DELLA protein of the common ancestor of land plants, and the importance of this function is underscored by its conservation over the past 450 million years.
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Affiliation(s)
- Jorge Hernández-García
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Rui Sun
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Antonio Serrano-Mislata
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Carlos Vargas-Chávez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig de la Barceloneta 37-49, Barcelona, Spain
| | - David Esteve-Bruna
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castellón de la Plana, Spain
| | - Shohei Yamaoka
- 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.
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universitat Politècnica de València), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
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25
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Kohchi T, Yamato KT, Ishizaki K, Yamaoka S, Nishihama R. Development and Molecular Genetics of Marchantia polymorpha. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:677-702. [PMID: 33684298 DOI: 10.1146/annurev-arplant-082520-094256] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.
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Affiliation(s)
- Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa 649-6493, Japan;
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
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26
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Romani F, Moreno JE. Molecular mechanisms involved in functional macroevolution of plant transcription factors. THE NEW PHYTOLOGIST 2021; 230:1345-1353. [PMID: 33368298 DOI: 10.1111/nph.17161] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/17/2020] [Indexed: 05/04/2023]
Abstract
Transcription factors (TFs) are key components of the transcriptional regulation machinery. In plants, they accompanied the evolution from unicellular aquatic algae to complex flowering plants that dominate the land environment. The adaptations of the body plan and physiological responses required changes in the biological functions of TFs. Some ancestral gene regulatory networks are highly conserved, while others evolved more recently and only exist in particular lineages. The recent emergence of novel model organisms provided the opportunity for comparative studies, producing new insights to infer these evolutionary trajectories. In this review, we comprehensively revisit the recent literature on TFs of nonseed plants and algae, focusing on the molecular mechanisms driving their functional evolution. We discuss the particular contribution of changes in DNA-binding specificity, protein-protein interactions and cis-regulatory elements to gene regulatory networks. Current advances have shown that these evolutionary processes were shaped by changes in TF expression pattern, not through great innovation in TF protein sequences. We propose that the role of TFs associated with environmental and developmental regulation was unevenly conserved during land plant evolution.
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Affiliation(s)
- Facundo Romani
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral - CONICET, Colectora RN 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Javier E Moreno
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral - CONICET, Colectora RN 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
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27
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Dijkhuizen LW, Tabatabaei BES, Brouwer P, Rijken N, Buijs VA, Güngör E, Schluepmann H. Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition. FRONTIERS IN PLANT SCIENCE 2021; 12:693039. [PMID: 34456937 PMCID: PMC8386757 DOI: 10.3389/fpls.2021.693039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/22/2021] [Indexed: 05/02/2023]
Abstract
Water ferns of the genus Azolla and the filamentous cyanobacteria Nostoc azollae constitute a model symbiosis that enabled the colonization of the water surface with traits highly desirable for the development of more sustainable crops: their floating mats capture CO2 and fix N2 at high rates using light energy. Their mode of sexual reproduction is heterosporous. The regulation of the transition from the vegetative phase to the spore forming phase in ferns is largely unknown, yet a prerequisite for Azolla domestication, and of particular interest as ferns represent the sister lineage of seed plants. Sporocarps induced with far red light could be crossed so as to verify species attribution of strains from the Netherlands but not of the strain from the Anzali lagoon in Iran; the latter strain was assigned to a novel species cluster from South America. Red-dominated light suppresses the formation of dissemination stages in both gametophyte- and sporophyte-dominated lineages of plants, the response likely is a convergent ecological strategy to open fields. FR-responsive transcripts included those from MIKCC homologues of CMADS1 and miR319-controlled GAMYB transcription factors in the fern, transporters in N. azollae, and ycf2 in chloroplasts. Loci of conserved microRNA (miRNA) in the fern lineage included miR172, yet FR only induced miR529 and miR535, and reduced miR319 and miR159. Phylogenomic analyses of MIKCC TFs suggested that the control of flowering and flower organ specification may have originated from the diploid to haploid phase transition in the homosporous common ancestor of ferns and seed plants.
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Affiliation(s)
- Laura W. Dijkhuizen
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Paul Brouwer
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Niels Rijken
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Valerie A. Buijs
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Erbil Güngör
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Henriette Schluepmann
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
- *Correspondence: Henriette Schluepmann
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28
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Biswal DP, Panigrahi KCS. Light- and hormone-mediated development in non-flowering plants: An overview. PLANTA 2020; 253:1. [PMID: 33245411 DOI: 10.1007/s00425-020-03501-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.
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Affiliation(s)
- Durga Prasad Biswal
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha, India
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kishore Chandra Sekhar Panigrahi
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha, India.
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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29
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Xu T, Yuan J, Hiltbrunner A. PHYTOCHROME INTERACTING FACTORs in the moss Physcomitrella patens regulate light-controlled gene expression. PHYSIOLOGIA PLANTARUM 2020; 169:467-479. [PMID: 32447760 DOI: 10.1111/ppl.13140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Phytochromes are red and far-red light receptors in plants that control growth and development in response to changes in the environment. Light-activated phytochromes enter the nucleus and act on a set of downstream signalling components to regulate gene expression. PHYTOCHROME INTERACTING FACTORs (PIFs) belong to the basic helix-loop-helix family of transcription factors and directly bind to light-activated phytochromes. Potential homologues of PIFs have been identified in ferns, bryophytes and streptophyte algae, and it has been shown that the potential PIF homologues from Physcomitrella patens, PIF1 to PIF4, have PIF function when expressed in Arabidopsis. However, their function in Physcomitrella is still unknown. Seed plant PIFs bind to G-box-containing promoters and, therefore, we searched the Physcomitrella genome for genes that contain G-boxes in their promoter. Here, we show that Physcomitrella PIFs activate these promoters in a G-box-dependent manner, suggesting that they could be direct PIF targets. Furthermore, we generated Physcomitrella pif1, pif2, pif3 and pif4 knock out mutant lines and quantified the expression of potential PIF direct target genes. The expression of these genes was generally reduced in pif mutants compared to the wildtype, but for several genes, the relative induction upon a short light treatment was higher in pif mutants than the wildtype. In contrast, expression of these genes was strongly repressed in continuous light, and pif mutants showed partial downregulation of these genes in the dark. Thus, the overall function of PIFs in light-regulated gene expression might be an ancient property of PIFs.
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Affiliation(s)
- Tengfei Xu
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinhong Yuan
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany
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30
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Lai X, Chahtane H, Martin-Arevalillo R, Zubieta C, Parcy F. Contrasted evolutionary trajectories of plant transcription factors. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:101-107. [PMID: 32417720 DOI: 10.1016/j.pbi.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.
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Affiliation(s)
- Xuelei Lai
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et de Développement des Plantes, INRAE, CNRS, ENS de Lyon, UCB Lyon 1, Université de Lyon, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France.
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31
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Menon C, Klose C, Hiltbrunner A. Arabidopsis FHY1 and FHY1-LIKE Are Not Required for Phytochrome A Signal Transduction in the Nucleus. PLANT COMMUNICATIONS 2020; 1:100007. [PMID: 33404546 PMCID: PMC7748001 DOI: 10.1016/j.xplc.2019.100007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/27/2019] [Accepted: 11/06/2019] [Indexed: 05/13/2023]
Abstract
Photoreceptors of the phytochrome family control a multitude of responses in plants. Phytochrome A (phyA) is essential for far-red light perception, which is important for germination and seedling establishment in strong canopy shade. Translocation of phyA from the cytosol into nucleus is a key step in far-red light signaling and requires FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). FHY1/FHL bind to phyA downstream signaling components. Therefore, it has been suggested that FHY1/FHL also have a function in assembling phyA transcription factor complexes in the nucleus. Yet, in this study, we show that constitutively nuclear-localized phyA is active in the absence of FHY1 and FHL. Furthermore, an artificial FHY1, consisting of an SV40 NLS, a phyA binding site, and a YFP tag as spacer between them, complements the fhy1-3 fhl-1 double mutant. These findings show that FHY1 and FHL are not required for phyA downstream signaling in the nucleus. However, we found that lines expressing phyA-NLS-YFP are hypersensitive to red and far-red light and that slightly increased levels of constitutively nuclear-localized phyA result in photomorphogenic development in the dark. Thus, restricting phyA to the cytosol and inducing nuclear transport in light by interaction with FHY1/FHL might be important to suppress photomorphogenesis in the dark.
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Affiliation(s)
- Chiara Menon
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Cornelia Klose
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Hiltbrunner
- Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Corresponding author
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32
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Koide E, Suetsugu N, Iwano M, Gotoh E, Nomura Y, Stolze SC, Nakagami H, Kohchi T, Nishihama R. Regulation of Photosynthetic Carbohydrate Metabolism by a Raf-Like Kinase in the Liverwort Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2020; 61:631-643. [PMID: 31851335 DOI: 10.1093/pcp/pcz232] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/12/2019] [Indexed: 05/27/2023]
Abstract
To optimize growth and development, plants monitor photosynthetic activities and appropriately regulate various cellular processes. However, signaling mechanisms that coordinate plant growth with photosynthesis remain poorly understood. To identify factors that are involved in signaling related to photosynthetic stimuli, we performed a phosphoproteomic analysis with Marchantia polymorpha, an extant bryophyte species in the basal lineage of land plants. Among proteins whose phosphorylation status changed differentially between dark-treated plants and those after light irradiation but failed to do so in the presence of a photosynthesis inhibitor, we identified a B4-group Raf-like kinase, named PHOTOSYNTHESIS-RELATED RAF (MpPRAF). Biochemical analyses confirmed photosynthesis-activity-dependent changes in the phosphorylation status of MpPRAF. Mutations in the MpPRAF gene resulted in growth retardation. Measurement of carbohydrates demonstrated both hyper-accumulation of starch and reduction of sucrose in Mppraf mutants. Neither inhibition of starch synthesis nor exogenous supply of sucrose alleviated the growth defect, suggesting serious impairment of Mppraf mutants in both the synthesis of sucrose and the repression of its catabolism. As a result of the compromised photosynthate metabolism, photosynthetic electron transport was downregulated in Mppraf mutants. A mutated MpPRAF with a common amino acid substitution for inactivating kinase activity was unable to rescue the Mppraf mutant defects. Our results provide evidence that MpPRAF is a photosynthesis signaling kinase that regulates sucrose metabolism.
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Affiliation(s)
- Eri Koide
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Megumi Iwano
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Eiji Gotoh
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, 230-0045 Japan
| | - Sara Christina Stolze
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, 230-0045 Japan
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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Naramoto S, Jones VAS, Trozzi N, Sato M, Toyooka K, Shimamura M, Ishida S, Nishitani K, Ishizaki K, Nishihama R, Kohchi T, Dolan L, Kyozuka J. A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs. PLoS Biol 2019; 17:e3000560. [PMID: 31815938 PMCID: PMC6901180 DOI: 10.1371/journal.pbio.3000560] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/11/2019] [Indexed: 12/26/2022] Open
Abstract
Land plant shoot structures evolved a diversity of lateral organs as morphological adaptations to the terrestrial environment, with lateral organs arising independently in different lineages. Vascular plants and bryophytes (basally diverging land plants) develop lateral organs from meristems of sporophytes and gametophytes, respectively. Understanding the mechanisms of lateral organ development among divergent plant lineages is crucial for understanding the evolutionary process of morphological diversification of land plants. However, our current knowledge of lateral organ differentiation mechanisms comes almost entirely from studies of seed plants, and thus, it remains unclear how these lateral structures evolved and whether common regulatory mechanisms control the development of analogous lateral organs. Here, we performed a mutant screen in the liverwort Marchantia polymorpha, a bryophyte, which produces gametophyte axes with nonphotosynthetic scalelike lateral organs. We found that an Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1 (ALOG) family protein, named M. polymorpha LATERAL ORGAN SUPRESSOR 1 (MpLOS1), regulates meristem maintenance and lateral organ development in Marchantia. A mutation in MpLOS1, preferentially expressed in lateral organs, induces lateral organs with misspecified identity and increased cell number and, furthermore, causes defects in apical meristem maintenance. Remarkably, MpLOS1 expression rescued the elongated spikelet phenotype of a MpLOS1 homolog in rice. This suggests that ALOG genes regulate the development of lateral organs in both gametophyte and sporophyte shoots by repressing cell divisions. We propose that the recruitment of ALOG-mediated growth repression was in part responsible for the convergent evolution of independently evolved lateral organs among highly divergent plant lineages, contributing to the morphological diversification of land plants. Ancestral land plants lacked leaves; instead, these evolved independently in each lineage and were key innovations that allowed the radiation of plants on land during the lower Palaeozoic. This study of the liverwort Marchantia polymorpha reveals that each time they evolved they used the same molecular mechanism to control leaf development.
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Affiliation(s)
- Satoshi Naramoto
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- * E-mail:
| | | | - Nicola Trozzi
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Masaki Shimamura
- Graduate School of Integrated Sciences for life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sakiko Ishida
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kazuhiko Nishitani
- Department of Biological Sciences, Kanagawa University, Hiratsuka, Japan
| | | | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants. Nat Commun 2019; 10:5219. [PMID: 31745087 PMCID: PMC6864062 DOI: 10.1038/s41467-019-13045-0] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 10/17/2019] [Indexed: 11/08/2022] Open
Abstract
Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.
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Tsuzuki M, Futagami K, Shimamura M, Inoue C, Kunimoto K, Oogami T, Tomita Y, Inoue K, Kohchi T, Yamaoka S, Araki T, Hamada T, Watanabe Y. An Early Arising Role of the MicroRNA156/529-SPL Module in Reproductive Development Revealed by the Liverwort Marchantia polymorpha. Curr Biol 2019; 29:3307-3314.e5. [PMID: 31543452 DOI: 10.1016/j.cub.2019.07.084] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/17/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
In angiosperms, the phase transition from vegetative to reproductive growth involves the de-repression of the squamosa promoter-binding-protein-like (SPL) class of transcription factors, which is negatively regulated by the specific microRNAs (miRNAs/miRs) miR156/529 [1]. Non-vascular land plants also undergo growth-phase transition to the reproductive state, but knowledge regarding the controlling mechanisms is limited. Here, we investigate the reproductive transition in the liverwort Marchantia polymorpha, focusing on the roles of miR529c [2-4] and MpSPL2. First, we established mir529c-null mutants using CRISPR/Cas9. Even in the absence of far-red light-supplemented long-day condition, which is usually needed to induce reproductive development [5, 6], the mutant thalli developed sexual reproductive organs (gametangia) and produced gametes. Transgenic plants expressing a miR529-resistant MpSPL2 transgene also showed a similar phenotype of reproductive transition in the absence of inductive far-red light signals. In these mutants and transgenic plants, the MpSPL2 mRNA abundance was elevated. Mpspl2ko mutant plants showed successful gamete development and fertilization, which suggests that MpSPL2 is involved in, but not essential for, sexual reproduction in M. polymorpha. Furthermore, analysis of Mpspl2ko mutant and its complemented lines suggests that MpSPL2 may have a role in promotion of reproductive transition. These findings support the notion that the transition to reproductive development in liverworts is controlled by a system similar to that in angiosperms, and the miR156/529-SPL module has common significance in the control of the vegetative-to-reproductive transition during development in many land plants, including liverworts.
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Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Kazutaka Futagami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Masaki Shimamura
- Department of Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Chikako Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kan Kunimoto
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi Oogami
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Tomita
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takahiro Hamada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan.
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
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