1
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Fukushima T, Kodama Y. Selection of a histidine auxotrophic Marchantia polymorpha strain with an auxotrophic selective marker. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:345-354. [PMID: 37283617 PMCID: PMC10240916 DOI: 10.5511/plantbiotechnology.22.0810a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/10/2022] [Indexed: 06/08/2023]
Abstract
Marchantia polymorpha has emerged as a model liverwort species, with molecular tools increasingly available. In the present study, we developed an auxotrophic strain of M. polymorpha and an auxotrophic selective marker gene as new experimental tools for this valuable model system. Using CRISPR (clustered regularly interspaced palindromic repeats)/Cas9-mediated genome editing, we mutated the genomic region for IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE (IGPD) in M. polymorpha to disrupt the biosynthesis of histidine (igpd). We modified an IGPD gene (IGPDm) with silent mutations, generating a histidine auxotrophic selective marker gene that was not a target of our CRISPR/Cas9-mediated genome editing. The M. polymorpha igpd mutant was a histidine auxotrophic strain, growing only on medium containing histidine. The igpd mutant could be complemented by transformation with the IGPDm gene, indicating that this gene could be used as an auxotrophic selective marker. Using the IGPDm marker in the igpd mutant background, we produced transgenic lines without the need for antibiotic selection. The histidine auxotrophic strain igpd and auxotrophic selective marker IGPDm represent new molecular tools for M. polymorpha research.
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Affiliation(s)
- Tatsushi Fukushima
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
- Graduate School of Regional Development and Creativity, Utsunomiya University, Tochigi 321-8505, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
- Graduate School of Regional Development and Creativity, Utsunomiya University, Tochigi 321-8505, Japan
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2
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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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3
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Takahashi H, Kodama Y. Culture-based preservation of Marchantia polymorpha gemmalings and thalli without encapsulation, drying, or freezing. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:449-452. [PMID: 35087310 PMCID: PMC8761591 DOI: 10.5511/plantbiotechnology.21.0902a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/02/2021] [Indexed: 06/08/2023]
Abstract
Ongoing research has generated many important lines of the model liverwort Marchantia polymorpha, including mutants and transgenic lines. To maintain these lines, researchers typically spend a lot of time and effort periodically replanting thalli (e.g., every month). To avoid this routine maintenance, researchers have developed methods for cryopreservation of dried and frozen gemmae. In this study, we developed a culture-based method for preserving gemmalings and thalli without encapsulation, drying, or freezing. The method requires only tissue culture on agar medium supplemented with sucrose in the dark at regular temperature (22°C). These culture conditions severely inhibit growth of gemmalings and thalli; however, these tissues remained alive after more than 1 year of storage. Survival rate of tissues using this method was 100% in all tests. This method thus enables preservation of gemmaling and thallus cultures on medium under regular temperature conditions, thereby relieving researchers of labor-intensive routine maintenance.
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Affiliation(s)
- Hitomi Takahashi
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
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Iwakawa H, Melkonian K, Schlüter T, Jeon HW, Nishihama R, Motose H, Nakagami H. Agrobacterium-Mediated Transient Transformation of Marchantia Liverworts. PLANT & CELL PHYSIOLOGY 2021; 62:1718-1727. [PMID: 34383076 DOI: 10.1093/pcp/pcab126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Agrobacterium-mediated transient gene expression is a rapid and useful approach for characterizing functions of gene products in planta. However, the practicability of the method in the model liverwort Marchantia polymorpha has not yet been thoroughly described. Here we report a simple and robust method for Agrobacterium-mediated transient transformation of Marchantia thalli and its applicability. When thalli of M. polymorpha were co-cultured with Agrobacterium tumefaciens carrying β-glucuronidase (GUS) genes, GUS staining was observed primarily in assimilatory filaments and rhizoids. GUS activity was detected 2 days after infection and saturated 3 days after infection. We were able to transiently co-express fluorescently tagged proteins with proper localizations. Furthermore, we demonstrate that our method can be used as a novel pathosystem to study liverwort-bacteria interactions. We also provide evidence that air chambers support bacterial colonization.
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Affiliation(s)
- Hidekazu Iwakawa
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Katharina Melkonian
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Titus Schlüter
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Hyung-Woo Jeon
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hiroyasu Motose
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
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Mohanasundaram B, Bhide AJ, Palit S, Chaturvedi G, Lingwan M, Masakapalli SK, Banerjee AK. The unique bryophyte-specific repeat-containing protein SHORT-LEAF regulates gametophore development in moss. PLANT PHYSIOLOGY 2021; 187:203-217. [PMID: 34618137 PMCID: PMC8418407 DOI: 10.1093/plphys/kiab261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/18/2021] [Indexed: 05/29/2023]
Abstract
Convergent evolution of shoot development across plant lineages has prompted numerous comparative genetic studies. Though functional conservation of gene networks governing flowering plant shoot development has been explored in bryophyte gametophore development, the role of bryophyte-specific genes remains unknown. Previously, we have reported Tnt1 insertional mutants of moss defective in gametophore development. Here, we report a mutant (short-leaf; shlf) having two-fold shorter leaves, reduced apical dominance, and low plasmodesmata frequency. UHPLC-MS/MS-based auxin quantification and analysis of soybean (Glycine max) auxin-responsive promoter (GH3:GUS) lines exhibited a striking differential auxin distribution pattern in the mutant gametophore. Whole-genome sequencing and functional characterization of candidate genes revealed that a novel bryophyte-specific gene (SHORT-LEAF; SHLF) is responsible for the shlf phenotype. SHLF represents a unique family of near-perfect tandem direct repeat (TDR)-containing proteins conserved only among mosses and liverworts, as evident from our phylogenetic analysis. Cross-complementation with a Marchantia homolog partially recovered the shlf phenotype, indicating possible functional specialization. The distinctive structure (longest known TDRs), absence of any known conserved domain, localization in the endoplasmic reticulum, and proteolytic cleavage pattern of SHLF imply its function in bryophyte-specific cellular mechanisms. This makes SHLF a potential candidate to study gametophore development and evolutionary adaptations of early land plants.
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Affiliation(s)
- Boominathan Mohanasundaram
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Amey J. Bhide
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Shirsa Palit
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Gargi Chaturvedi
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Maneesh Lingwan
- School of Basic Sciences, Indian Institute of Technology (IIT), Himachal Pradesh, Mandi 175005, India
| | - Shyam Kumar Masakapalli
- School of Basic Sciences, Indian Institute of Technology (IIT), Himachal Pradesh, Mandi 175005, India
| | - Anjan K. Banerjee
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
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6
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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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Lin L, Ma J, Ai Q, Pritchard HW, Li W, Chen H. Lipid Remodeling Confers Osmotic Stress Tolerance to Embryogenic Cells during Cryopreservation. Int J Mol Sci 2021; 22:2174. [PMID: 33671662 PMCID: PMC7926411 DOI: 10.3390/ijms22042174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
Plant species conservation through cryopreservation using plant vitrification solutions (PVS) is based in empiricism and the mechanisms that confer cell integrity are not well understood. Using ESI-MS/MS analysis and quantification, we generated 12 comparative lipidomics datasets for membranes of embryogenic cells (ECs) of Magnolia officinalis during cryogenic treatments. Each step of the complex PVS-based cryoprotocol had a profoundly different impact on membrane lipid composition. Loading treatment (osmoprotection) remodeled the cell membrane by lipid turnover, between increased phosphatidic acid (PA) and phosphatidylglycerol (PG) and decreased phosphatidylcholine (PC) and phosphatidylethanolamine (PE). The PA increase likely serves as an intermediate for adjustments in lipid metabolism to desiccation stress. Following PVS treatment, lipid levels increased, including PC and PE, and this effectively counteracted the potential for massive loss of lipid species when cryopreservation was implemented in the absence of cryoprotection. The present detailed cryobiotechnology findings suggest that the remodeling of membrane lipids and attenuation of lipid degradation are critical for the successful use of PVS. As lipid metabolism and composition varies with species, these new insights provide a framework for technology development for the preservation of other species at increasing risk of extinction.
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Affiliation(s)
- Liang Lin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (L.L.); (J.M.); (Q.A.); (H.W.P.)
| | - Junchao Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (L.L.); (J.M.); (Q.A.); (H.W.P.)
| | - Qin Ai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (L.L.); (J.M.); (Q.A.); (H.W.P.)
| | - Hugh W. Pritchard
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (L.L.); (J.M.); (Q.A.); (H.W.P.)
- Royal Botanic Gardens, Kew, Wellcome Trust Millennium Building, Wakehurst Place, West Sussex, Ardingly RH17 6TN, UK
| | - Weiqi Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (L.L.); (J.M.); (Q.A.); (H.W.P.)
| | - Hongying Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (L.L.); (J.M.); (Q.A.); (H.W.P.)
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Takahashi H, Kodama Y. CRUNC: a cryopreservation method for unencapsulated gemmae of Marchantia polymorpha. PeerJ 2020; 8:e10174. [PMID: 33150079 PMCID: PMC7587056 DOI: 10.7717/peerj.10174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/22/2020] [Indexed: 01/20/2023] Open
Abstract
Genetic modifications such as mutation and transformation are powerful tools to study the function of genes and proteins in the model liverwort Marchantia polymorpha, but maintaining the resulting germplasm requires a practical, reliable method. Cryopreservation methods allow researchers to maintain mutant and transgenic lines of M. polymorpha. To date, two methods have been developed for cryopreservation of M. polymorpha gemmae: in the first method, unencapsulated gemmae are stored in liquid nitrogen at −196 °C, and in the second method, encapsulated gemmae are stored in liquid nitrogen at −196 °C or a deep freezer at −80 °C. In the present study, we developed a simple method named CRUNC (cr yopreservation of un en c apsulated gemmae), which can be used to store unencapsulated, dried gemmae of wild-type and transgenic M. polymorpha lines in liquid nitrogen and in freezers at −80 °C and −20 °C. Using the CRUNC method, we observed a high recovery rate (as high as 100%) and successful long-term (5 months) storage of the gemmae. Therefore, the CRUNC method is practical for maintaining valuable M. polymorpha germplasm.
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Affiliation(s)
- Hitomi Takahashi
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
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Sauret-Güeto S, Frangedakis E, Silvestri L, Rebmann M, Tomaselli M, Markel K, Delmans M, West A, Patron NJ, Haseloff J. Systematic Tools for Reprogramming Plant Gene Expression in a Simple Model, Marchantia polymorpha. ACS Synth Biol 2020; 9:864-882. [PMID: 32163700 DOI: 10.1021/acssynbio.9b00511] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present the OpenPlant toolkit, a set of interlinked resources and techniques to develop Marchantia as testbed for bioengineering in plants. Marchantia is a liverwort, a simple plant with an open form of development that allows direct visualization of gene expression and dynamics of cellular growth in living tissues. We describe new techniques for simple and efficient axenic propagation and maintenance of Marchantia lines with no requirement for glasshouse facilities. Marchantia plants spontaneously produce clonal propagules within a few weeks of regeneration, and lines can be amplified million-fold in a single generation by induction of the sexual phase of growth, crossing, and harvesting of progeny spores. The plant has a simple morphology and genome with reduced gene redundancy, and the dominant phase of its life cycle is haploid, making genetic analysis easier. We have built robust Loop assembly vector systems for nuclear and chloroplast transformation and genome editing. These have provided the basis for building and testing a modular library of standardized DNA elements with highly desirable properties. We have screened transcriptomic data to identify a range of candidate genes, extracted putative promoter sequences, and tested them in vivo to identify new constitutive promoter elements. The resources have been combined into a toolkit for plant bioengineering that is accessible for laboratories without access to traditional facilities for plant biology research. The toolkit is being made available under the terms of the OpenMTA and will facilitate the establishment of common standards and the use of this simple plant as testbed for synthetic biology.
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Affiliation(s)
- Susanna Sauret-Güeto
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Eftychios Frangedakis
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Linda Silvestri
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, U.K
| | - Marius Rebmann
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Kasey Markel
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | | | | | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
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Hamashima N, Xie X, Hikawa M, Suzuki T, Kodama Y. A gain-of-function T-DNA insertion mutant of Marchantia polymorpha hyper-accumulates flavonoid riccionidin A. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:201-204. [PMID: 31768123 PMCID: PMC6854341 DOI: 10.5511/plantbiotechnology.19.0722a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/22/2019] [Indexed: 05/09/2023]
Abstract
Marchantia polymorpha is a model liverwort for which many molecular biological techniques are now available. We previously developed the S-AgarTrap method for easy genetic transformation of M. polymorpha using spores. In this study, we report production of a T-DNA insertion mutant library (approx. 10,000 lines) for M. polymorpha using the S-AgarTrap method. We further isolate and characterize a gain-of-function mutant that hyper-accumulates the flavonoid riccionidin A. The present study demonstrates that the S-AgarTrap-mediated production of a T-DNA insertion mutant library is a powerful tool for molecular biology in M. polymorpha.
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Affiliation(s)
- Noriko Hamashima
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
| | - Xiaonan Xie
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
| | - Mio Hikawa
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
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Togawa T, Adachi T, Harada D, Mitani T, Tanaka D, Ishizaki K, Kohchi T, Yamato KT. Cryopreservation of Marchantia polymorpha spermatozoa. JOURNAL OF PLANT RESEARCH 2018; 131:1047-1054. [PMID: 30066035 DOI: 10.1007/s10265-018-1059-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The liverwort Marchantia polymorpha has become one of the model organisms, since it has less genetic redundancy, sexual and asexual modes of reproduction and a range of genomic and molecular genetic resources. Cryopreservation of fertile spermatozoa eliminates time, space and labor for growing and maintaining male plants in reproductive phase, and also provides an optional way to backup lines. Here we report a protocol to cryopreserve spermatozoa of M. polymorpha in liquid nitrogen. A cryoprotective solution containing sucrose, glycerol and egg yolk and controlled cooling and warming processes led to successful recovery of motile M. polymorpha spermatozoa after the cryogenic process. The survival rate and average motility of spermatozoa after cryopreservation were maintained at 71 and 54% of those before cryopreservation, respectively. Cryopreserved spermatozoa were capable of fertilization to form normal spores. The technique presented here confers more versatility to experiments using M. polymorpha and could be applied to preservation of plant spermatozoa in general.
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Affiliation(s)
- Taisuke Togawa
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, 649-6493, Japan
| | - Tohru Adachi
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, 649-6493, Japan
| | - Daijiro Harada
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, 649-6493, Japan
| | - Tasuku Mitani
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, 649-6493, Japan
- Institute of Advanced Technology, Kindai University, Kainan, Wakayama, 642-0017, Japan
| | - Daisuke Tanaka
- IBBP Center, National Institute for Basic Biology, Okazaki, Aichi, 444-8787, Japan
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - 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, Wakayama, 649-6493, Japan.
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12
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Novel gateway binary vectors for rapid tripartite DNA assembly and promoter analysis with various reporters and tags in the liverwort Marchantia polymorpha. PLoS One 2018; 13:e0204964. [PMID: 30286137 PMCID: PMC6171868 DOI: 10.1371/journal.pone.0204964] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/16/2018] [Indexed: 01/09/2023] Open
Abstract
The liverwort Marchantia polymorpha is an emerging model species for basal lineage plant research. In this study, two Gateway cloning-compatible binary vector series, R4pMpGWB and R4L1pMpGWB, were generated to facilitate production of transgenic M. polymorpha. The R4pMpGWB series allows tripartite recombination of any promoter and any coding sequence with a specific reporter or tag. Reporters/tags for the R4pMpGWB series are GUS, ELuc(PEST), FLAG, 3×HA, 4×Myc, mRFP1, Citrine, mCitrine, ER-targeted mCitrine and nucleus-targeted mCitrine. The R4L1pMpGWB series is suitable for promoter analysis. R4L1pMpGWB vector structure is the same as that of R4pMpGWB vectors, except that the attR2 site is replaced with attL1, enabling bipartite recombination of any promoter with a reporter or tag. Reporters/tags for the R4L1pMpGWB series are GUS, G3GFP-GUS, LUC, ELuc(PEST), Citrine, mCitrine, ER-targeted mCitrine and mCitrine-NLS. Both vector series were functional in M. polymorpha cells. These vectors will facilitate the design and assembly of plasmid constructs and generation of transgenic M. polymorpha.
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13
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Mechanisms Underlying Freezing and Desiccation Tolerance in Bryophytes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:167-187. [DOI: 10.1007/978-981-13-1244-1_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Tanaka D, Niino T, Uemura M. Cryopreservation of Plant Genetic Resources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:355-369. [PMID: 30288719 DOI: 10.1007/978-981-13-1244-1_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cryopreservation encompasses several interconnect disciplines including physiology and cryophysics. This chapter reviews the current techniques for cryopreservation of plant genetic resources (PGRs). Vitrification is an effective ice crystal avoidance mechanism for hydrated cells and tissues. With any cryopreservation method, whole or partial parts of specimens which are sufficiently dehydrated can be vitrified by rapid cooling in liquid nitrogen (LN). Techniques discussed are the vitrification protocol, encapsulation-vitrification protocol, droplet vitrification protocol (DV), vitrification protocol using cryo-plates (V cryo-plate), and air dehydration protocol using cryo-plates (D cryo-plate). In these DV, V, and D cryo-plate protocols, specimens to be cryopreserved are immersed directly into LN on aluminum foil strips or cryo-plates; removal from LN to rewarming solution results in a high level of plant regrowth with ultrarapid cooling and warming. The protocols were applied to a wide array of plant species including wild and multi-ploid species, although fine tuning of the protocols was required for successful application to specific plant species and lines. These three protocols efficiently complement each other and appear highly promising to facilitate large-scale cryobanking of PGRs in genebanks. Cryo-scanning electron microscopy makes it possible to examine the cellular and water behavior in plant tissues when immersed in LN. It has been verified that tissues cryopreserved by the process of vitrification and the cryo-plate protocols are cryopreservation methods for reliable long-term preservation of PGRs.
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Affiliation(s)
- Daisuke Tanaka
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Japan.
| | - Takao Niino
- Gene Research Center, University of Tsukuba, Tsukuba, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences and Department of Plant-biosciences, Faculty of Agriculture, Iwate University, Morioka, Japan
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15
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Sugano SS, Nishihama R. CRISPR/Cas9-Based Genome Editing of Transcription Factor Genes in Marchantia polymorpha. Methods Mol Biol 2018; 1830:109-126. [PMID: 30043367 DOI: 10.1007/978-1-4939-8657-6_7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Plant transcription factors (TFs) belong to a wide variety of gene families. The systematic and rapid establishment of knockout lines of TF genes is critical for functional genetics. Genome engineering techniques for dissecting out the molecular function of TFs have been dramatically improved by CRISPR/Cas9-based genome editing technology. In the CRISPR/Cas9 system, Cas9 functions as a Cas9-gRNA ribonucleoprotein complex and uses its DNA endonuclease activity to induce the cleavage of the genome, which is targeted by gRNA. Double-strand breaks sometimes induce insertions and deletions at the target site, leading to frameshift mutations of TF genes. In this chapter, we describe a detailed protocol for the targeted mutagenesis of TFs using the CRISPR/Cas9 system, specifically in the case of Marchantia polymorpha, an emerging model plant for functional genomics. The CRISPR/Cas9 system is highly versatile for targeting genomic sequences because only an alteration of the gRNA sequence is needed to change target sequences. The labor and cost required to establish genome-edited lines are low enough that multiple mutants of TF genes can be generated in one laboratory. The CRISPR/Cas9-based genome editing technique consists of four steps: (1) gRNA design; (2) vector construction; (3) transformation; and (4) isolation of genome-edited lines. This manuscript focuses mainly on the strategy of gRNA design, the workflow for off-target searches, and the selection and identification of genome-edited lines by genotyping. Although we describe a protocol for M. polymorpha, the basic strategy of generating genome-edited lines of TF genes should be applicable widely to other plants.
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Affiliation(s)
- Shigeo S Sugano
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Shiga, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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16
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Ohyanagi H, Obayashi T, Yano K. Editorial: Plant and Cell Physiology's 2017 Database Issue. PLANT & CELL PHYSIOLOGY 2017; 58:1-3. [PMID: 28158372 DOI: 10.1093/pcp/pcw227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Hajime Ohyanagi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Takeshi Obayashi
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Kentaro Yano
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
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17
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Ishizaki K, Nishihama R, Yamato KT, Kohchi T. Molecular Genetic Tools and Techniques for Marchantia polymorpha Research. PLANT & CELL PHYSIOLOGY 2016; 57:262-70. [PMID: 26116421 DOI: 10.1093/pcp/pcv097] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/18/2015] [Indexed: 05/18/2023]
Abstract
Liverworts occupy a basal position in the evolution of land plants, and are a key group to address a wide variety of questions in plant biology. Marchantia polymorpha is a common, easily cultivated, dioecious liverwort species, and is emerging as an experimental model organism. The haploid gametophytic generation dominates the diploid sporophytic generation in its life cycle. Genetically homogeneous lines in the gametophyte generation can be established easily and propagated through asexual reproduction, which aids genetic and biochemical experiments. Owing to its dioecy, male and female sexual organs are formed in separate individuals, which enables crossing in a fully controlled manner. Reproductive growth can be induced at the desired times under laboratory conditions, which helps genetic analysis. The developmental process from a single-celled spore to a multicellular body can be observed directly in detail. As a model organism, molecular techniques for M. polymorpha are well developed; for example, simple and efficient protocols of Agrobacterium-mediated transformation have been established. Based on them, various strategies for molecular genetics, such as introduction of reporter constructs, overexpression, gene silencing and targeted gene modification, are available. Herein, we describe the technologies and resources for reverse and forward genetics in M. polymorpha, which offer an excellent experimental platform to study the evolution and diversity of regulatory systems in land plants.
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Affiliation(s)
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kinki University, Wakayama, 649-6493 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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18
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Bowman JL, Araki T, Kohchi T. Marchantia: Past, Present and Future. PLANT & CELL PHYSIOLOGY 2016; 57:205-9. [PMID: 26889047 DOI: 10.1093/pcp/pcw023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
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