1
|
Sessa G, Carabelli M, Sassi M. The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development. Int J Mol Sci 2024; 25:5657. [PMID: 38891845 PMCID: PMC11171833 DOI: 10.3390/ijms25115657] [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: 04/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.
Collapse
Affiliation(s)
| | | | - Massimiliano Sassi
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy; (G.S.); (M.C.)
| |
Collapse
|
2
|
Schmidt V, Skokan R, Depaepe T, Kurtović K, Haluška S, Vosolsobě S, Vaculíková R, Pil A, Dobrev PI, Motyka V, Van Der Straeten D, Petrášek J. Phytohormone profiling in an evolutionary framework. Nat Commun 2024; 15:3875. [PMID: 38719800 PMCID: PMC11079000 DOI: 10.1038/s41467-024-47753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/09/2024] [Indexed: 05/12/2024] Open
Abstract
The genomes of charophyte green algae, close relatives of land plants, typically do not show signs of developmental regulation by phytohormones. However, scattered reports of endogenous phytohormone production in these organisms exist. We performed a comprehensive analysis of multiple phytohormones in Viridiplantae, focusing mainly on charophytes. We show that auxin, salicylic acid, ethylene and tRNA-derived cytokinins including cis-zeatin are found ubiquitously in Viridiplantae. By contrast, land plants but not green algae contain the trans-zeatin type cytokinins as well as auxin and cytokinin conjugates. Charophytes occasionally produce jasmonates and abscisic acid, whereas the latter is detected consistently in land plants. Several phytohormones are excreted into the culture medium, including auxin by charophytes and cytokinins and salicylic acid by Viridiplantae in general. We note that the conservation of phytohormone biosynthesis and signaling pathways known from angiosperms does not match the capacity for phytohormone biosynthesis in Viridiplantae. Our phylogenetically guided analysis of established algal cultures provides an important insight into phytohormone biosynthesis and metabolism across Streptophyta.
Collapse
Affiliation(s)
- Vojtěch Schmidt
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czechia
- Department of Experimental Plant Biology, Charles University, Viničná 5, 128 44, Prague 2, Czechia
| | - Roman Skokan
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czechia.
| | - Thomas Depaepe
- Laboratory of Functional Plant Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Katarina Kurtović
- Department of Experimental Plant Biology, Charles University, Viničná 5, 128 44, Prague 2, Czechia
| | - Samuel Haluška
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czechia
- Department of Experimental Plant Biology, Charles University, Viničná 5, 128 44, Prague 2, Czechia
| | - Stanislav Vosolsobě
- Department of Experimental Plant Biology, Charles University, Viničná 5, 128 44, Prague 2, Czechia
| | - Roberta Vaculíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czechia
| | - Anthony Pil
- Laboratory of Functional Plant Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Petre Ivanov Dobrev
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czechia
| | - Václav Motyka
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czechia
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Jan Petrášek
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czechia.
- Department of Experimental Plant Biology, Charles University, Viničná 5, 128 44, Prague 2, Czechia.
| |
Collapse
|
3
|
Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Dhabalia Ashok A, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nat Genet 2024; 56:1018-1031. [PMID: 38693345 PMCID: PMC11096116 DOI: 10.1038/s41588-024-01737-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]
Abstract
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
Collapse
Affiliation(s)
- Xuehuan Feng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Zhejiang Lab, Hanzhou, China
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum Hamburg, Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Yunnan, China
| | - Bo Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jaccoline M S Zegers
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maaike J Bierenbroodspot
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture 'La Mayora', Málaga, Spain
| | - Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Jeffrey P Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University, Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg and Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Xiyin Wang
- North China University of Science and Technology, Tangshan, China
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE, USA
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- University of Goettingen, Goettingen Center for Molecular Biosciences, Goettingen, Germany.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
| |
Collapse
|
4
|
Flores-Sandoval E, Nishihama R, Bowman JL. Hormonal and genetic control of pluripotency in bryophyte model systems. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102486. [PMID: 38041967 DOI: 10.1016/j.pbi.2023.102486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 12/04/2023]
Abstract
Land plant meristems are reservoirs of pluripotent stem cells where new tissues emerge, grow and eventually differentiate into specific cell identities. Compared to algae, where cells are produced in two-dimensional tissues via tip or marginal growth, land plants have meristems that allow three-dimensional growth for successful exploration of the terrestrial environment. In land plants, meristem maintenance leads to indeterminate growth and the production of new meristems leads to branching or regeneration via reprogramming of wounded somatic cells. Emerging model systems in the haploid dominant and monophyletic bryophytes are allowing comparative analyses of meristem gene regulatory networks to address whether all plants use common or diverse programs to organise, maintain, and regenerate meristems. In this piece we aim to discuss recent advances in genetic and hormonal control of bryophyte meristems and possible convergence or discrepancies in an exciting and emerging field in plant biology.
Collapse
Affiliation(s)
- 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.
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - 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
| |
Collapse
|
5
|
Wójcikowska B, Belaidi S, Robert HS. Game of thrones among AUXIN RESPONSE FACTORs-over 30 years of MONOPTEROS research. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6904-6921. [PMID: 37450945 PMCID: PMC10690734 DOI: 10.1093/jxb/erad272] [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: 02/28/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
For many years, research has been carried out with the aim of understanding the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review summarizes over 30 years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, namely embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and, finally, all the genes under its direct control. In addition, information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years.
Collapse
Affiliation(s)
- Barbara Wójcikowska
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Samia Belaidi
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| |
Collapse
|
6
|
Huang C, Jin X, Lin H, He J, Chen Y. Comparative Transcriptome Sequencing and Endogenous Phytohormone Content of Annual Grafted Branches of Zelkova schneideriana and Its Dwarf Variety HenTianGao. Int J Mol Sci 2023; 24:16902. [PMID: 38069226 PMCID: PMC10706849 DOI: 10.3390/ijms242316902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Zelkova schneideriana is a fast-growing tree species endemic to China. Recent surveys and reports have highlighted a continued decline in its natural populations; therefore, it is included in the Red List of Threatened Species by The International Union for Conservation of Nature. A new variety "HenTianGao" (H) has been developed with smaller plant height, slow growth, and lower branching points. In this study, we attempted to understand the differences in plant height of Z. schneideriana (J) and its dwarf variety H. We determined the endogenous hormone content in the annual grafted branches of both J and H. J exhibited higher gibberellic acid (GA)-19 and trans-Zeatin (tZ) levels, whereas H had higher levels of indole-3-acetic acid (IAA) catabolite 2-oxindole-3-acetic acid (OxIAA), IAA-Glu conjugate, and jasmonic acid (JA) (and its conjugate JA-Ile). The transcriptome comparison showed differential regulation of 20,944 genes enriched in growth and development, signaling, and metabolism-related pathways. The results show that the differential phytohormone level (IAA, JA, tZ, and GA) was consistent with the expression of the genes associated with their biosynthesis. The differences in relative OxIAA, IAA-Glu, GA19, trans-Zeatin, JA, and JA-Ile levels were linked to changes in respective signaling-related genes. We also observed significant differences in the expression of cell size, number, proliferation, cell wall biosynthesis, and remodeling-related genes in J and H. The differences in relative endogenous hormone levels, expression of biosynthesis, and signaling genes provide a theoretical basis for understanding the plant height differences in Z. schneideriana.
Collapse
Affiliation(s)
- Chenfei Huang
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (C.H.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
| | - Xiaoling Jin
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (C.H.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
| | - Haiyan Lin
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Jinsong He
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (C.H.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
| | - Yan Chen
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (C.H.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
| |
Collapse
|
7
|
Carrillo-Carrasco VP, Hernández-García J, Weijers D. Electroporation-based delivery of proteins in Penium margaritaceum and other zygnematophycean algae. PHYSIOLOGIA PLANTARUM 2023; 175:e14121. [PMID: 38148204 DOI: 10.1111/ppl.14121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]
Abstract
Zygnematophycean algae represent the streptophyte group identified as the closest sister clade to land plants. Their phylogenetic position and growing genomic resources make these freshwater algae attractive models for evolutionary studies in the context of plant terrestrialization. However, available genetic transformation protocols are limited and exclusively DNA-based. To expand the zygnematophycean toolkit, we developed a DNA-free method for protein delivery into intact cells using electroporation. We use confocal microscopy coupled with fluorescence lifetime imaging to assess the delivery of mNeonGreen into algal cells. We optimized the method to obtain high efficiency of delivery and cell recovery after electroporation in two strains of Penium margaritaceum and show that the experimental setup can also be used to deliver proteins in other zygnematophycean species such as Closterium peracerosum-strigosum-littorale complex and Mesotaenium endlicherianum. We discuss the possible applications of this proof-of-concept method.
Collapse
Affiliation(s)
| | | | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| |
Collapse
|
8
|
Dadras A, Fürst-Jansen JMR, Darienko T, Krone D, Scholz P, Sun S, Herrfurth C, Rieseberg TP, Irisarri I, Steinkamp R, Hansen M, Buschmann H, Valerius O, Braus GH, Hoecker U, Feussner I, Mutwil M, Ischebeck T, de Vries S, Lorenz M, de Vries J. Environmental gradients reveal stress hubs pre-dating plant terrestrialization. NATURE PLANTS 2023; 9:1419-1438. [PMID: 37640935 PMCID: PMC10505561 DOI: 10.1038/s41477-023-01491-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unravelled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum. Here we used fine-combed RNA sequencing in tandem with a photophysiological assessment on Mesotaenium exposed to a continuous range of temperature and light cues. Our data establish a grid of 42 different conditions, resulting in 128 transcriptomes and ~1.5 Tbp (~9.9 billion reads) of data to study the combinatory effects of stress response using clustering along gradients. Mesotaenium shares with land plants major hubs in genetic networks underpinning stress response and acclimation. Our data suggest that lipid droplet formation and plastid and cell wall-derived signals have denominated molecular programmes since more than 600 million years of streptophyte evolution-before plants made their first steps on land.
Collapse
Affiliation(s)
- Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Denis Krone
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Patricia Scholz
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
| | - Siqi Sun
- Institute of Plant Biology and Biotechnology, Green Biotechnology, University of Münster, Münster, Germany
| | - Cornelia Herrfurth
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Rasmus Steinkamp
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maike Hansen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences, Biocenter, University of Cologne, Cologne, Germany
| | - Henrik Buschmann
- Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Oliver Valerius
- Institute of Microbiology and Genetics and Göttingen Center for Molecular Biosciences and Service Unit LCMS Protein Analytics, Department of Molecular Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Gerhard H Braus
- Institute of Microbiology and Genetics and Göttingen Center for Molecular Biosciences and Service Unit LCMS Protein Analytics, Department of Molecular Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences, Biocenter, University of Cologne, Cologne, Germany
| | - Ivo Feussner
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Till Ischebeck
- Institute of Plant Biology and Biotechnology, Green Biotechnology, University of Münster, Münster, Germany
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maike Lorenz
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Experimental Phycology and SAG Culture Collection of Algae, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- Goettingen Center for Molecular Biosciences, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
| |
Collapse
|
9
|
Powell AE, Heyl A. The origin and early evolution of cytokinin signaling. FRONTIERS IN PLANT SCIENCE 2023; 14:1142748. [PMID: 37457338 PMCID: PMC10338860 DOI: 10.3389/fpls.2023.1142748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/23/2023] [Indexed: 07/18/2023]
Abstract
Angiosperms, especially Arabidopsis and rice, have long been at the center of plant research. However, technological advances in sequencing have led to a dramatic increase in genome and transcriptome data availability across land plants and, more recently, among green algae. These data allowed for an in-depth study of the evolution of different protein families - including those involved in the metabolism and signaling of phytohormones. While most early studies on phytohormone evolution were phylogenetic, those studies have started to be complemented by genetic and biochemical studies in recent years. Examples of such functional analyses focused on ethylene, jasmonic acid, abscisic acid, and auxin. These data have been summarized recently. In this review, we will focus on the progress in our understanding of cytokinin biology. We will use these data to synthesize key points about the evolution of cytokinin metabolism and signaling, which might apply to the evolution of other phytohormones as well.
Collapse
|
10
|
Khan SI, Yamada R, Shiroma R, Abe T, Kozaki A. Properties of INDETERMINATE DOMAIN Proteins from Physcomitrium patens: DNA-Binding, Interaction with GRAS Proteins, and Transcriptional Activity. Genes (Basel) 2023; 14:1249. [PMID: 37372429 DOI: 10.3390/genes14061249] [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: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
INDETERMINATE DOMAIN (IDD) proteins are plant-specific transcription factors that interact with GRAS proteins, such as DELLA and SHORT ROOT (SHR), to regulate target genes. The combination of IDD and DELLA proteins regulates genes involved in gibberellic acid (GA) synthesis and GA signaling, whereas the combination of IDD with the complex of SHR and SCARECROW, another GRAS protein, regulates genes involved in root tissue formation. Previous bioinformatic research identified seven IDDs, two DELLA, and two SHR genes in Physcomitrium patens, a model organism for non-vascular plants (bryophytes), which lack a GA signaling pathway and roots. In this study, DNA-binding properties and protein-protein interaction of IDDs from P. patens (PpIDD) were analyzed. Our results showed that the DNA-binding properties of PpIDDs were largely conserved between moss and seed plants. Four PpIDDs showed interaction with Arabidopsis DELLA (AtDELLA) proteins but not with PpDELLAs, and one PpIDD showed interaction with PpSHR but not with AtSHR. Moreover, AtIDD10 (JACKDAW) interacted with PpSHR but not with PpDELLAs. Our results indicate that DELLA proteins have modified their structure to interact with IDD proteins during evolution from moss lineage to seed plants, whereas the interaction of IDD and SHR was already present in moss lineage.
Collapse
Affiliation(s)
- Saiful Islam Khan
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ren Yamada
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ryoichi Shiroma
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tatsuki Abe
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Akiko Kozaki
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| |
Collapse
|
11
|
Bai Y, Dou Y, Xie Y, Zheng H, Gao J. Phylogeny, transcriptional profile, and auxin-induced phosphorylation modification characteristics of conserved PIN proteins in Moso bamboo (Phyllostachys edulis). Int J Biol Macromol 2023; 234:123671. [PMID: 36801226 DOI: 10.1016/j.ijbiomac.2023.123671] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Auxin polar transport is an important way for auxin to exercise its function, and auxin plays an irreplaceable role in the rapid growth of Moso bamboo. We identified and performed the structural analysis of PIN-FORMED auxin efflux carriers in Moso bamboo and obtained a total of 23 PhePIN genes from five gene subfamilies. We also performed chromosome localization and intra- and inter-species synthesis analysis. Phylogenetic analyses of 216 PIN genes showed that PIN genes are relatively conserved in the evolution of the Bambusoideae and have undergone intra-family segment replication in Moso bamboo. The PIN genes' transcriptional patterns showed that the PIN1 subfamily plays a major regulatory role. PIN genes and auxin biosynthesis maintain a high degree of consistency in spatial and temporal distribution. Phosphoproteomics analysis identified many phosphorylated protein kinases that respond to auxin regulation through autophosphorylation and phosphorylation of PIN proteins. The protein interaction network showed that there is a plant hormone interaction regulatory network with PIN protein as the core. We provide a comprehensive PIN protein analysis that complements the auxin regulatory pathway in Moso bamboo and paves the way for further auxin regulatory studies in bamboo.
Collapse
Affiliation(s)
- Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Yuping Dou
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China.
| |
Collapse
|
12
|
Suzuki H, Kato H, Iwano M, Nishihama R, Kohchi T. Auxin signaling is essential for organogenesis but not for cell survival in the liverwort Marchantia polymorpha. THE PLANT CELL 2023; 35:1058-1075. [PMID: 36529527 PMCID: PMC10015169 DOI: 10.1093/plcell/koac367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/28/2022] [Accepted: 12/15/2022] [Indexed: 05/12/2023]
Abstract
Auxin plays pleiotropic roles in plant development via gene regulation upon its perception by the receptors TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFBs). This auxin-regulated transcriptional control mechanism originated in the common ancestor of land plants. Although the complete loss of TIR1/AFBs causes embryonic lethality in Arabidopsis thaliana, it is unclear whether the requirement for TIR1-mediated auxin perception in cell viability can be generalized. The model liverwort Marchantia polymorpha has a minimal auxin signaling system with only a single TIR1/AFB, MpTIR1. Here we show by genetic, biochemical, and transcriptomic analyses that MpTIR1 functions as an evolutionarily conserved auxin receptor. Null mutants and conditionally knocked-out mutants of MpTIR1 were viable but incapable of forming any organs and grew as cell masses. Principal component analysis performed using transcriptomes at various developmental stages indicated that MpTIR1 is involved in the developmental transition from spores to organized thalli, during which apical notches containing stem cells are established. In Mptir1 cells, stem cell- and differentiation-related genes were up- and downregulated, respectively. Our findings suggest that, in M. polymorpha, auxin signaling is dispensable for cell division but is essential for three-dimensional patterning of the plant body by establishing pluripotent stem cells for organogenesis, a derived trait of land plants.
Collapse
Affiliation(s)
- Hidemasa Suzuki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Hirotaka Kato
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Megumi Iwano
- 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
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
13
|
Rieseberg TP, Dadras A, Fürst-Jansen JMR, Dhabalia Ashok A, Darienko T, de Vries S, Irisarri I, de Vries J. Crossroads in the evolution of plant specialized metabolism. Semin Cell Dev Biol 2023; 134:37-58. [PMID: 35292191 DOI: 10.1016/j.semcdb.2022.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 12/25/2022]
Abstract
The monophyletic group of embryophytes (land plants) stands out among photosynthetic eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety, embryophytes account for the majority of the biomass on land and constitute an astounding biodiversity. What allowed for the massive radiation of this particular lineage? One of the defining features of all land plants is the production of an array of specialized metabolites. The compounds that the specialized metabolic pathways of embryophytes produce have diverse functions, ranging from superabundant structural polymers and compounds that ward off abiotic and biotic challenges, to signaling molecules whose abundance is measured at the nanomolar scale. These specialized metabolites govern the growth, development, and physiology of land plants-including their response to the environment. Hence, specialized metabolites define the biology of land plants as we know it. And they were likely a foundation for their success. It is thus intriguing to find that the closest algal relatives of land plants, freshwater organisms from the grade of streptophyte algae, possess homologs for key enzymes of specialized metabolic pathways known from land plants. Indeed, some studies suggest that signature metabolites emerging from these pathways can be found in streptophyte algae. Here we synthesize the current understanding of which routes of the specialized metabolism of embryophytes can be traced to a time before plants had conquered land.
Collapse
Affiliation(s)
- Tim P Rieseberg
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtsr. 1, 37077 Goettingen, Germany.
| |
Collapse
|
14
|
Leong R, Tan JJ, Koh SS, Wu TY, Ishizaki K, Urano D. G protein signaling and metabolic pathways as evolutionarily conserved mechanisms to combat calcium deficiency. THE NEW PHYTOLOGIST 2023; 237:615-630. [PMID: 36266966 DOI: 10.1111/nph.18561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Calcium (Ca) deficiency causes necrotic symptoms of foliar edges known as tipburn; however, the underlying cellular mechanisms have been poorly understood due to the lack of an ideal plant model and research platform. Using a phenotyping system that quantitates growth and tipburn traits in the model bryophyte Marchantia polymorpha, we evaluated metabolic compounds and the Gβ-null mutant (gpb1) that modulate the occurrence and expansion of the tipburn. Transcriptomic comparisons between wild-type and gpb1 plants revealed the phenylalanine/phenylpropanoid biosynthesis pathway and reactive oxygen species (ROS) important for Ca deficiency responses. gpb1 plants reduced ROS production possibly through transcriptomic regulations of class III peroxidases and induced the expression of phenylpropanoid pathway enzymes without changing downstream lignin contents. Supplementation of intermediate metabolites and chemical inhibitors further confirmed the cell-protective mechanisms of the phenylpropanoid and ROS pathways. Marchantia polymorpha, Arabidopsis thaliana, and Lactuca sativa showed comparable transcriptomic changes where genes related to phenylpropanoid and ROS pathways were enriched in response to Ca deficiency. In conclusion, our study demonstrated unresolved signaling and metabolic pathways of Ca deficiency response. The phenotyping platform can speed up the discovery of chemical and genetic pathways, which could be widely conserved between M. polymorpha and angiosperms.
Collapse
Affiliation(s)
- Richalynn Leong
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore City, Singapore
| | - Javier Jingheng Tan
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
| | - Sally Shuxian Koh
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore City, Singapore
| | - Ting-Ying Wu
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Daisuke Urano
- Temasek Life Sciences Laboratory Ltd, National University of Singapore, 1 Research Link, 117604, Singapore City, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore City, Singapore
- Singapore-MIT Alliance for Research and Technology, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore City, Singapore
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Bonhomme S, Guillory A. Synthesis and signalling of strigolactone and KAI2-ligand signals in bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4487-4495. [PMID: 35524989 DOI: 10.1093/jxb/erac186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
Strigolactones (SLs), long known as butenolide rhizospheric signals, have been recognized since 2008 as a class of hormones regulating many aspects of plant development. Many authors also anticipate 'KAI2-ligand' (KL) as a novel class of phytohormones; however, this ligand remains elusive. Core genes of SL and KL pathways, first described in angiosperms, are found in all land plants and some even in green algae. This review reports current knowledge of these pathways in bryophytes. Data on the pathways mostly come from two models: the moss Physcomitrium patens and the liverwort Marchantia. Gene targeting methods have allowed functional analyses of both models. Recent work in Marchantia suggests that SLs' ancestral role was to recruit beneficial microbes as arbuscular mycorrhizal fungi. In contrast, the hormonal role of SLs observed in P. patens is probably a result of convergent evolution. Evidence for a functional KL pathway in both bryophyte models is very recent. Nevertheless, many unknowns remain and warrant a more extensive investigation of SL and KL pathways in various land plant lineages.
Collapse
Affiliation(s)
- Sandrine Bonhomme
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Ambre Guillory
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
- Laboratoire des Interactions Plantes - Microbes - Environnement (LIPME), Université de Toulouse, INRAE, CNRS, 24 Chemin de Borde Rouge, 31320 Castanet-Tolosan, France
| |
Collapse
|
17
|
Dani KGS, Loreto F. Plant volatiles as regulators of hormone homeostasis. THE NEW PHYTOLOGIST 2022; 234:804-812. [PMID: 35170033 DOI: 10.1111/nph.18035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Some canonical plant hormones such as auxins and gibberellins have precursors that are biogenic volatiles (indole, indole acetonitrile, phenylacetaldoxime and ent-kaurene). Cytokinins, abscisic acid and strigolactones are hormones comprising chemical moieties that have distinct volatile analogues, and are synthesised alongside constitutively emitted volatiles (isoprene, sesquiterpenes, lactones, benzenoids and apocarotenoid volatiles). Nonvolatile hormone analogues and biogenic volatile organic compounds (BVOCs) evolved in tandem as growth and behavioural regulators in unicellular organisms. In plants, however, nonvolatile hormones evolved as regulators of growth, development and differentiation, while endogenous BVOCs (often synthesised lifelong) became subtle regulators of hormone synthesis, availability, activity and turnover, all supported by functionally redundant components of hormone metabolism. Reciprocal changes in the abundance and activity of hormones, nitric oxide, and constitutive plant volatiles constantly bridge retrograde and anterograde signalling to maintain hormone equilibria even in unstressed plants. This is distinct from transient interference in hormone signalling by stress-induced and exogenously received volatiles.
Collapse
Affiliation(s)
- Kaidala Ganesha Srikanta Dani
- Institute of Sustainable Plant Protection, National Research Council of Italy, Via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy
- Department of Biology, Agriculture and Food Sciences, National Research Council of Italy, Piazzale Aldo Moro 7, Rome, 00185, Italy
| | - Francesco Loreto
- Institute of Sustainable Plant Protection, National Research Council of Italy, Via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia, Naples, 80126, Italy
| |
Collapse
|
18
|
Guillory A, Bonhomme S. Phytohormone biosynthesis and signaling pathways of mosses. PLANT MOLECULAR BIOLOGY 2021; 107:245-277. [PMID: 34245404 DOI: 10.1007/s11103-021-01172-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Most known phytohormones regulate moss development. We present a comprehensive view of the synthesis and signaling pathways for the most investigated of these compounds in mosses, focusing on the model Physcomitrium patens. The last 50 years of research have shown that most of the known phytohormones are synthesized by the model moss Physcomitrium patens (formerly Physcomitrella patens) and regulate its development, in interaction with responses to biotic and abiotic stresses. Biosynthesis and signaling pathways are best described in P. patens for the three classical hormones auxins, cytokinins and abscisic acid. Furthermore, their roles in almost all steps of development, from early filament growth to gametophore development and sexual reproduction, have been the focus of much research effort over the years. Evidence of hormonal roles exist for ethylene and for CLE signaling peptides, as well as for salicylic acid, although their possible effects on development remain unclear. Production of brassinosteroids by P. patens is still debated, and modes of action for these compounds are even less known. Gibberellin biosynthesis and signaling may have been lost in P. patens, while gibberellin precursors such as ent-kaurene derivatives could be used as signals in a yet to discover pathway. As for jasmonic acid, it is not used per se as a hormone in P. patens, but its precursor OPDA appears to play a corresponding role in defense against abiotic stress. We have tried to gather a comprehensive view of the biosynthesis and signaling pathways for all these compounds in mosses, without forgetting strigolactones, the last class of plant hormones to be reported. Study of the strigolactone response in P. patens points to a novel signaling compound, the KAI2-ligand, which was likely employed as a hormone prior to land plant emergence.
Collapse
Affiliation(s)
- Ambre Guillory
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France
| | - Sandrine Bonhomme
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France.
| |
Collapse
|
19
|
Abstract
There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.
Collapse
Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jordi Paps
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
| |
Collapse
|
20
|
Fichtner F, Dissanayake IM, Lacombe B, Barbier F. Sugar and Nitrate Sensing: A Multi-Billion-Year Story. TRENDS IN PLANT SCIENCE 2021; 26:352-374. [PMID: 33281060 DOI: 10.1016/j.tplants.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/23/2020] [Accepted: 11/04/2020] [Indexed: 05/03/2023]
Abstract
Sugars and nitrate play a major role in providing carbon and nitrogen in plants. Understanding how plants sense these nutrients is crucial, most notably for crop improvement. The mechanisms underlying sugar and nitrate sensing are complex and involve moonlighting proteins such as the nitrate transporter NRT1.1/NFP6.3 or the glycolytic enzyme HXK1. Major components of nutrient signaling, such as SnRK1, TOR, and HXK1, are relatively well conserved across eukaryotes, and the diversification of components such as the NRT1 family and the SWEET sugar transporters correlates with plant terrestrialization. In plants, Tre6P plays a hormone-like role in plant development. In addition, nutrient signaling has evolved to interact with the more recent hormone signaling, allowing fine-tuning of physiological and developmental responses.
Collapse
Affiliation(s)
- Franziska Fichtner
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Benoit Lacombe
- Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Francois Barbier
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| |
Collapse
|
21
|
Isoda R, Yoshinari A, Ishikawa Y, Sadoine M, Simon R, Frommer WB, Nakamura M. Sensors for the quantification, localization and analysis of the dynamics of plant hormones. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:542-557. [PMID: 33231903 PMCID: PMC7898640 DOI: 10.1111/tpj.15096] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/19/2020] [Indexed: 05/13/2023]
Abstract
Plant hormones play important roles in plant growth and development and physiology, and in acclimation to environmental changes. The hormone signaling networks are highly complex and interconnected. It is thus important to not only know where the hormones are produced, how they are transported and how and where they are perceived, but also to monitor their distribution quantitatively, ideally in a non-invasive manner. Here we summarize the diverse set of tools available for quantifying and visualizing hormone distribution and dynamics. We provide an overview over the tools that are currently available, including transcriptional reporters, degradation sensors, and luciferase and fluorescent sensors, and compare the tools and their suitability for different purposes.
Collapse
Affiliation(s)
- Reika Isoda
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Akira Yoshinari
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Yuuma Ishikawa
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Mayuri Sadoine
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Rüdiger Simon
- Developmental GeneticsHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Wolf B. Frommer
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Masayoshi Nakamura
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| |
Collapse
|
22
|
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: 7] [Impact Index Per Article: 1.8] [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.
Collapse
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.
| |
Collapse
|
23
|
Israeli A, Reed JW, Ori N. Genetic dissection of the auxin response network. NATURE PLANTS 2020; 6:1082-1090. [PMID: 32807951 DOI: 10.1038/s41477-020-0739-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/06/2020] [Indexed: 05/24/2023]
Abstract
The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.
Collapse
Affiliation(s)
- Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, Rehovot, Israel
| | - Jason W Reed
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, Rehovot, Israel.
| |
Collapse
|
24
|
de Vries J, de Vries S, Curtis BA, Zhou H, Penny S, Feussner K, Pinto DM, Steinert M, Cohen AM, von Schwartzenberg K, Archibald JM. Heat stress response in the closest algal relatives of land plants reveals conserved stress signaling circuits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1025-1048. [PMID: 32333477 DOI: 10.1111/tpj.14782] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/28/2020] [Accepted: 04/08/2020] [Indexed: 05/20/2023]
Abstract
All land plants (embryophytes) share a common ancestor that likely evolved from a filamentous freshwater alga. Elucidating the transition from algae to embryophytes - and the eventual conquering of Earth's surface - is one of the most fundamental questions in plant evolutionary biology. Here, we investigated one of the organismal properties that might have enabled this transition: resistance to drastic temperature shifts. We explored the effect of heat stress in Mougeotia and Spirogyra, two representatives of Zygnematophyceae - the closest known algal sister lineage to land plants. Heat stress induced pronounced phenotypic alterations in their plastids, and high-performance liquid chromatography-tandem mass spectroscopy-based profiling of 565 transitions for the analysis of main central metabolites revealed significant shifts in 43 compounds. We also analyzed the global differential gene expression responses triggered by heat, generating 92.8 Gbp of sequence data and assembling a combined set of 8905 well-expressed genes. Each organism had its own distinct gene expression profile; less than one-half of their shared genes showed concordant gene expression trends. We nevertheless detected common signature responses to heat such as elevated transcript levels for molecular chaperones, thylakoid components, and - corroborating our metabolomic data - amino acid metabolism. We also uncovered the heat-stress responsiveness of genes for phosphorelay-based signal transduction that links environmental cues, calcium signatures and plastid biology. Our data allow us to infer the molecular heat stress response that the earliest land plants might have used when facing the rapidly shifting temperature conditions of the terrestrial habitat.
Collapse
Affiliation(s)
- Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, 37077, Goettingen, Germany
| | - Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitätsstr. 1, 40225, Duesseldorf, Germany
| | - Bruce A Curtis
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
| | - Hong Zhou
- Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Institute of Plant Science and Microbiology, Universität Hamburg, 22609, Hamburg, Germany
| | - Susanne Penny
- National Research Council, Human Health Therapeutics, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), 37077, Goettingen, Germany
| | - Devanand M Pinto
- National Research Council, Human Health Therapeutics, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, NS, B3H 4R2, Canada
| | - Michael Steinert
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Alejandro M Cohen
- Biological Spectrometry Core Facility, Life Sciences Research Institute, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Klaus von Schwartzenberg
- Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Institute of Plant Science and Microbiology, Universität Hamburg, 22609, Hamburg, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Canadian Institute for Advanced Research, 661 University Ave, Suite 505, Toronto, ON, M5G 1M1, Canada
| |
Collapse
|
25
|
McAdam SAM, Sussmilch FC. The evolving role of abscisic acid in cell function and plant development over geological time. Semin Cell Dev Biol 2020; 109:39-45. [PMID: 32571626 DOI: 10.1016/j.semcdb.2020.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023]
Abstract
Abscisic acid (ABA) is found in a wide diversity of organisms, yet we know most about the hormonal action of this compound in the ecologically dominant and economically important angiosperms. In angiosperms, ABA regulates a suite of critical responses from desiccation tolerance through to seed dormancy and stomatal closure. Work exploring the function of key genes in the ABA signalling pathway of angiosperms has revealed that this signal transduction pathway is ancient, yet considerable change in the physiological roles of this hormone have occurred over geological time. With recent advances in our capacity to characterise gene function in non-angiosperms we are on the cusp of revealing the origins of this critical hormonal signalling pathway in plants, and understanding how a simple hormone may have shaped land plant diversity, ecology and adaptation over the past 500 million years.
Collapse
Affiliation(s)
- Scott A M McAdam
- Purdue Center for Plant Biology, Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Frances C Sussmilch
- School of Natural Sciences, University of Tasmania, Sandy Bay, TAS, 7005, Australia
| |
Collapse
|
26
|
Cesarino I, Dello Ioio R, Kirschner GK, Ogden MS, Picard KL, Rast-Somssich MI, Somssich M. Plant science's next top models. ANNALS OF BOTANY 2020; 126:1-23. [PMID: 32271862 PMCID: PMC7304477 DOI: 10.1093/aob/mcaa063] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models. SCOPE Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers. CONCLUSIONS Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.
Collapse
Affiliation(s)
- Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão 277, Butantã, São Paulo, Brazil
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Gwendolyn K Kirschner
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Division of Crop Functional Genomics, Bonn, Germany
| | - Michael S Ogden
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Kelsey L Picard
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Madlen I Rast-Somssich
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, VIC, Australia
| | - Marc Somssich
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
27
|
Jiao C, Sørensen I, Sun X, Sun H, Behar H, Alseekh S, Philippe G, Palacio Lopez K, Sun L, Reed R, Jeon S, Kiyonami R, Zhang S, Fernie AR, Brumer H, Domozych DS, Fei Z, Rose JKC. The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants. Cell 2020; 181:1097-1111.e12. [PMID: 32442406 DOI: 10.1016/j.cell.2020.04.019] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/14/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
The evolutionary features and molecular innovations that enabled plants to first colonize land are not well understood. Here, insights are provided through our report of the genome sequence of the unicellular alga Penium margaritaceum, a member of the Zygnematophyceae, the sister lineage to land plants. The genome has a high proportion of repeat sequences that are associated with massive segmental gene duplications, likely facilitating neofunctionalization. Compared with representatives of earlier diverging algal lineages, P. margaritaceum has expanded repertoires of gene families, signaling networks, and adaptive responses that highlight the evolutionary trajectory toward terrestrialization. These encompass a broad range of physiological processes and protective cellular features, such as flavonoid compounds and large families of modifying enzymes involved in cell wall biosynthesis, assembly, and remodeling. Transcriptome profiling further elucidated adaptations, responses, and selective pressures associated with the semi-terrestrial ecosystems of P. margaritaceum, where a simple body plan would be an advantage.
Collapse
Affiliation(s)
- Chen Jiao
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Hila Behar
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, BC V6T 1Z3, Canada
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Li Sun
- Skidmore College, Saratoga Springs, NY, USA
| | | | - Susan Jeon
- Skidmore College, Saratoga Springs, NY, USA
| | - Reiko Kiyonami
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA, USA
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, BC V6T 1Z3, Canada; Department of Botany, University of British Columbia, 3200-6270 University Blvd., Vancouver, BC V6H 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA; U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
28
|
Prigge MJ, Platre M, Kadakia N, Zhang Y, Greenham K, Szutu W, Pandey BK, Bhosale RA, Bennett MJ, Busch W, Estelle M. Genetic analysis of the Arabidopsis TIR1/AFB auxin receptors reveals both overlapping and specialized functions. eLife 2020; 9:54740. [PMID: 32067636 PMCID: PMC7048394 DOI: 10.7554/elife.54740] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/04/2020] [Indexed: 01/03/2023] Open
Abstract
The TIR1/AFB auxin co-receptors mediate diverse responses to the plant hormone auxin. The Arabidopsis genome encodes six TIR1/AFB proteins representing three of the four clades that were established prior to angiosperm radiation. To determine the role of these proteins in plant development we performed an extensive genetic analysis involving the generation and characterization of all possible multiply-mutant lines. We find that loss of all six TIR1/AFB proteins results in early embryo defects and eventually seed abortion, and yet a single wild-type allele of TIR1 or AFB2 is sufficient to support growth throughout development. Our analysis reveals extensive functional overlap between even the most distantly related TIR1/AFB genes except for AFB1. Surprisingly, AFB1 has a specialized function in rapid auxin-dependent inhibition of root growth and early phase of root gravitropism. This activity may be related to a difference in subcellular localization compared to the other members of the family.
Collapse
Affiliation(s)
- Michael J Prigge
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Matthieu Platre
- Plant Molecular and Cellular Biology Laboratory and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Nikita Kadakia
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Yi Zhang
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Kathleen Greenham
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Whitnie Szutu
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| | - Bipin Kumar Pandey
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Rahul Arvind Bhosale
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Malcolm J Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Mark Estelle
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, United States
| |
Collapse
|
29
|
Wang S, Li L, Li H, Sahu SK, Wang H, Xu Y, Xian W, Song B, Liang H, Cheng S, Chang Y, Song Y, Çebi Z, Wittek S, Reder T, Peterson M, Yang H, Wang J, Melkonian B, Van de Peer Y, Xu X, Wong GKS, Melkonian M, Liu H, Liu X. Genomes of early-diverging streptophyte algae shed light on plant terrestrialization. NATURE PLANTS 2020; 6:95-106. [PMID: 31844283 PMCID: PMC7027972 DOI: 10.1038/s41477-019-0560-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/28/2019] [Indexed: 05/18/2023]
Abstract
Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.
Collapse
Affiliation(s)
- Sibo Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linzhou Li
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haoyuan Li
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hongli Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wenfei Xian
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Hongping Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shifeng Cheng
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Zehra Çebi
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Sebastian Wittek
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Tanja Reder
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Morten Peterson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Barbara Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB/UGent Center for Plant Systems Biology, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Shenzhen, China.
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany.
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| |
Collapse
|
30
|
Bartlett M. Looking back to look forward: protein-protein interactions and the evolution of development. THE NEW PHYTOLOGIST 2020; 225:1127-1133. [PMID: 31494948 DOI: 10.1111/nph.16179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
The evolutionary modification of development was fundamental in generating extant plant diversity. Similarly, the modification of development is a path forward to engineering the plants of the future, provided we know enough about what to modify. Understanding how extant diversity was generated will reveal productive pathways forward for modifying development. Here, I discuss four examples of developmental pathways that have been remodeled by changes to protein-protein interactions. These are cases where changes to developmental pathways have been paralleled by recent changes, selected for or engineered by humans. Extant plant diversity represents a vast treasure trove of molecular solutions to ecological problems. Mining this treasure trove will allow for the intentional modification of plant development for solving future problems.
Collapse
Affiliation(s)
- Madelaine Bartlett
- University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 2, Amherst, MA, 01003, USA
| |
Collapse
|
31
|
Wang L, Zou Y, Kaw HY, Wang G, Sun H, Cai L, Li C, Meng LY, Li D. Recent developments and emerging trends of mass spectrometric methods in plant hormone analysis: a review. PLANT METHODS 2020; 16:54. [PMID: 32322293 PMCID: PMC7161177 DOI: 10.1186/s13007-020-00595-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 04/04/2020] [Indexed: 05/18/2023]
Abstract
Plant hormones are naturally occurring small molecule compounds which are present at trace amounts in plant. They play a pivotal role in the regulation of plant growth. The biological activity of plant hormones depends on their concentrations in the plant, thus, accurate determination of plant hormone is paramount. However, the complex plant matrix, wide polarity range and low concentration of plant hormones are the main hindrances to effective analyses of plant hormone even when state-of-the-art analytical techniques are employed. These factors substantially influence the accuracy of analytical results. So far, significant progress has been realized in the analysis of plant hormones, particularly in sample pretreatment techniques and mass spectrometric methods. This review describes the classic extraction and modern microextraction techniques used to analyze plant hormone. Advancements in solid phase microextraction (SPME) methods have been driven by the ever-increasing requirement for dynamic and in vivo identification of the spatial distribution of plant hormones in real-life plant samples, which would contribute greatly to the burgeoning field of plant hormone investigation. In this review, we describe advances in various aspects of mass spectrometry methods. Many fragmentation patterns are analyzed to provide the theoretical basis for the establishment of a mass spectral database for the analysis of plant hormones. We hope to provide a technical guide for further discovery of new plant hormones. More than 140 research studies on plant hormone published in the past decade are reviewed, with a particular emphasis on the recent advances in mass spectrometry and sample pretreatment techniques in the analysis of plant hormone. The potential progress for further research in plant hormones analysis is also highlighted.
Collapse
Affiliation(s)
- Liyuan Wang
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Yilin Zou
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Han Yeong Kaw
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Gang Wang
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Huaze Sun
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Long Cai
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| | - Chengyu Li
- State Key Laboratory of Application of Rare Earth Resources, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Long-Yue Meng
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
- Department of Environmental Science, Yanbian University, Yanji, 133002 China
| | - Donghao Li
- Department of Chemistry, MOE Key Laboratory of Biological Resources of the Changbai Mountain and Functional Molecules, Yanbian University, Park Road 977, Yanji, 133002 China
| |
Collapse
|
32
|
Evolution of the Auxin Response Factors from charophyte ancestors. PLoS Genet 2019; 15:e1008400. [PMID: 31553720 PMCID: PMC6797205 DOI: 10.1371/journal.pgen.1008400] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/17/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
Auxin is a major developmental regulator in plants and the acquisition of a transcriptional response to auxin likely contributed to developmental innovations at the time of water-to-land transition. Auxin Response Factors (ARFs) Transcription Factors (TFs) that mediate auxin-dependent transcriptional changes are divided into A, B and C evolutive classes in land plants. The origin and nature of the first ARF proteins in algae is still debated. Here, we identify the most ‘ancient’ ARF homologue to date in the early divergent charophyte algae Chlorokybus atmophyticus, CaARF. Structural modelling combined with biochemical studies showed that CaARF already shares many features with modern ARFs: it is capable of oligomerization, interacts with the TOPLESS co-repressor and specifically binds Auxin Response Elements as dimer. In addition, CaARF possesses a DNA-binding specificity that differs from class A and B ARFs and that was maintained in class C ARF along plants evolution. Phylogenetic evidence together with CaARF biochemical properties indicate that the different classes of ARFs likely arose from an ancestral proto-ARF protein with class C-like features. The foundation of auxin signalling would have thus happened from a pre-existing hormone-independent transcriptional regulation together with the emergence of a functional hormone perception complex. Plants transition from water to land was determining for the history of our planet, since it led to atmospheric and soil condition changes that promoted the appearance of other life forms. This transition initiated around 1 billion years ago from a Charophyte algae lineage that acquired features allowing it to adapt to the very different terrestrial conditions. Land plants coordinate their development with external stimuli through signalling mechanisms triggered by plant hormones. Therefore, evolution of these molecules and their signalling pathways likely played an important role in the aquatic to terrestrial move. In this manuscript we study the origin of auxin signalling, a plant hormone implicated in all plant developmental steps. Our studies suggest that out of the three families of proteins originally proposed to trigger auxin signalling in land plants, only one existed in Charophyte ancestors as a likely transcriptional repressor independent of auxin. We show that despite millions of years of evolution, this family of proteins has conserved its biochemical and structural properties that are found today in land plants. The results presented here provide an insight on how hormone signalling pathways could have evolved by co-opting a pre-existing hormone-independent transcriptional regulatory mechanism.
Collapse
|
33
|
Sauer M, Kleine-Vehn J. PIN-FORMED and PIN-LIKES auxin transport facilitators. Development 2019; 146:146/15/dev168088. [PMID: 31371525 DOI: 10.1242/dev.168088] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The phytohormone auxin influences virtually all aspects of plant growth and development. Auxin transport across membranes is facilitated by, among other proteins, members of the PIN-FORMED (PIN) and the structurally similar PIN-LIKES (PILS) families, which together govern directional cell-to-cell transport and intracellular accumulation of auxin. Canonical PIN proteins, which exhibit a polar localization in the plasma membrane, determine many patterning and directional growth responses. Conversely, the less-studied non-canonical PINs and PILS proteins, which mostly localize to the endoplasmic reticulum, attenuate cellular auxin responses. Here, and in the accompanying poster, we provide a brief summary of current knowledge of the structure, evolution, function and regulation of these auxin transport facilitators.
Collapse
Affiliation(s)
- Michael Sauer
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|
34
|
de Vries S, de Vries J, Rose LE. The Elaboration of miRNA Regulation and Gene Regulatory Networks in Plant⁻Microbe Interactions. Genes (Basel) 2019; 10:genes10040310. [PMID: 31010062 PMCID: PMC6523410 DOI: 10.3390/genes10040310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plants are exposed to diverse abiotic and biotic stimuli. These require fast and specific integrated responses. Such responses are coordinated at the protein and transcript levels and are incorporated into larger regulatory networks. Here, we focus on the evolution of transcriptional regulatory networks involved in plant–pathogen interactions. We discuss the evolution of regulatory networks and their role in fine-tuning plant defense responses. Based on the observation that many of the cornerstones of immune signaling in angiosperms are also present in streptophyte algae, it is likely that some regulatory components also predate the origin of land plants. The degree of functional conservation of many of these ancient components has not been elucidated. However, ongoing functional analyses in bryophytes show that some components are conserved. Hence, some of these regulatory components and how they are wired may also trace back to the last common ancestor of land plants or earlier. Of course, an understanding of the similarities and differences during the evolution of plant defense networks cannot ignore the lineage-specific coevolution between plants and their pathogens. In this review, we specifically focus on the small RNA regulatory networks involved in fine-tuning of the strength and timing of defense responses and highlight examples of pathogen exploitation of the host RNA silencing system. These examples illustrate well how pathogens frequently target gene regulation and thereby alter immune responses on a larger scale. That this is effective is demonstrated by the diversity of pathogens from distinct kingdoms capable of manipulating the same gene regulatory networks, such as the RNA silencing machinery.
Collapse
Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, 38106 Braunschweig, Germany.
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
- CEPLAS-Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany.
| |
Collapse
|
35
|
Roeder AH, Jill Harrison C. Editorial overview: Scaling development through the plant tree of life. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:A1-A4. [PMID: 30850085 DOI: 10.1016/j.pbi.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Adrienne Hk Roeder
- Weill Institute for Cell and Molecular Biology and Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
| |
Collapse
|