1
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Uyehara AN, Diep BN, Allsman LA, Gayer SG, Martinez SE, Kim JJ, Agarwal S, Rasmussen CG. De Novo TANGLED1 Recruitment to Aberrant Cell Plate Fusion Sites in Maize. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583939. [PMID: 38496554 PMCID: PMC10942460 DOI: 10.1101/2024.03.07.583939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Division plane positioning is critical for proper growth and development in many organisms. In plants, the division plane is established before mitosis, by accumulation of a cytoskeletal structure called the preprophase band (PPB). The PPB is thought to be essential for recruitment of division site localized proteins, which remain at the division site after the PPB disassembles. Here, we show that a division site localized protein, TANGLED1 (TAN1), is recruited independently of the PPB to the cell cortex at sites, by the plant cytokinetic machinery, the phragmoplast. TAN1 recruitment to de novo sites on the cortex is partially dependent on intact actin filaments and the myosin XI motor protein OPAQUE1 (O1). These data imply a yet unknown role for TAN1 and possibly other division site localized proteins during the last stages of cell division when the phragmoplast touches the cell cortex to complete cytokinesis.
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Affiliation(s)
- Aimee N. Uyehara
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
| | - Beatrice N. Diep
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
- Current address: Cellular and Molecular Biology Graduate Program, University of Wisconsin, Madison, WI, USA 53706
| | - Lindy A. Allsman
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
| | - Sarah G. Gayer
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
| | - Stephanie E. Martinez
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
| | - Janice J. Kim
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
| | - Shreya Agarwal
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
| | - Carolyn G. Rasmussen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA, USA 92521
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2
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Lu YT, Loue-Manifel J, Bollier N, Gadient P, De Winter F, Carella P, Hoguin A, Grey-Switzman S, Marnas H, Simon F, Copin A, Fischer S, de Leau E, Schornack S, Nishihama R, Kohchi T, Depège Fargeix N, Ingram G, Nowack MK, Goodrich J. Convergent evolution of water-conducting cells in Marchantia recruited the ZHOUPI gene promoting cell wall reinforcement and programmed cell death. Curr Biol 2024; 34:793-807.e7. [PMID: 38295796 DOI: 10.1016/j.cub.2024.01.014] [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: 08/30/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
A key adaptation of plants to life on land is the formation of water-conducting cells (WCCs) for efficient long-distance water transport. Based on morphological analyses it is thought that WCCs have evolved independently on multiple occasions. For example, WCCs have been lost in all but a few lineages of bryophytes but, strikingly, within the liverworts a derived group, the complex thalloids, has evolved a novel externalized water-conducting tissue composed of reinforced, hollow cells termed pegged rhizoids. Here, we show that pegged rhizoid differentiation in Marchantia polymorpha is controlled by orthologs of the ZHOUPI and ICE bHLH transcription factors required for endosperm cell death in Arabidopsis seeds. By contrast, pegged rhizoid development was not affected by disruption of MpNAC5, the Marchantia ortholog of the VND genes that control WCC formation in flowering plants. We characterize the rapid, genetically controlled programmed cell death process that pegged rhizoids undergo to terminate cellular differentiation and identify a corresponding upregulation of conserved putative plant cell death effector genes. Lastly, we show that ectopic expression of MpZOU1 increases production of pegged rhizoids and enhances drought tolerance. Our results support that pegged rhizoids evolved independently of other WCCs. We suggest that elements of the genetic control of developmental cell death are conserved throughout land plants and that the ZHOUPI/ICE regulatory module has been independently recruited to promote cell wall modification and programmed cell death in liverwort rhizoids and in the endosperm of flowering plant seed.
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Affiliation(s)
- Yen-Ting Lu
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Jeanne Loue-Manifel
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK; Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69342, France
| | | | - Philippe Gadient
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | | | - Philip Carella
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Antoine Hoguin
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Shona Grey-Switzman
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Hugo Marnas
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Francois Simon
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Alice Copin
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Shelby Fischer
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Erica de Leau
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - 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
| | - Nathalie Depège Fargeix
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69342, France
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69342, France
| | - Moritz K Nowack
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
| | - Justin Goodrich
- Institute of Molecular Plant Science, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
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3
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Gao F, Dubos C. The arabidopsis bHLH transcription factor family. TRENDS IN PLANT SCIENCE 2023:S1360-1385(23)00381-3. [PMID: 38143207 DOI: 10.1016/j.tplants.2023.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023]
Abstract
Basic helix-loop-helices (bHLHs) are present in all eukaryotes and form one of the largest families of transcription factors (TFs) found in plants. bHLHs function as transcriptional activators and/or repressors of genes involved in key processes involved in plant growth and development in interaction with the environment (e.g., stomata and root hair development, iron homeostasis, and response to heat and shade). Recent studies have improved our understanding of the functioning of bHLH TFs in complex regulatory networks where a series of post-translational modifications (PTMs) have critical roles in regulating their subcellular localization, DNA-binding capacity, transcriptional activity, and/or stability (e.g., protein-protein interactions, phosphorylation, ubiquitination, and sumoylation). Further elucidating the function and regulation of bHLHs will help further understanding of the biology of plants in general and for the development of new tools for crop improvement.
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Affiliation(s)
- Fei Gao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; Yuelushan Laboratory, Changsha 410128, China.
| | - Christian Dubos
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
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4
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Smit ME, Bergmann DC. The stomatal fates: Understanding initiation and enforcement of stomatal cell fate transitions. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102449. [PMID: 37709566 DOI: 10.1016/j.pbi.2023.102449] [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: 06/05/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
In the stomatal lineage, repeated arcs of initiation, stem-cell proliferation, and terminal cell fate commitment are displayed on the surface of aerial organs. Over the past two decades, the core transcription and signaling elements that guide cell divisions, patterning, and fate transitions were defined. Here we highlight recent work that extends the core using a variety of cutting-edge techniques in different plant species. New work has discovered transcriptional circuits that initiate and reinforce stomatal fate transitions, while also enabling the lineage to interpret and respond to environmental inputs. Recent developments show that some key stomatal factors are more flexible or potentially even interchangeable, opening up avenues to explore stomatal fates and regulatory networks.
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Affiliation(s)
- Margot E Smit
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Dominique C Bergmann
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305-5020, USA.
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5
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Kongsted TE, Glover BJ. Phylogenetic analysis of bHLH classes III and IV in land plants and their algal relatives. THE NEW PHYTOLOGIST 2023; 240:1717-1721. [PMID: 37578088 DOI: 10.1111/nph.19202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Affiliation(s)
- Thea E Kongsted
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Beverley J Glover
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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6
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Lee YS, Shiu SH, Grotewold E. Evolution and diversification of the ACT-like domain associated with plant basic helix-loop-helix transcription factors. Proc Natl Acad Sci U S A 2023; 120:e2219469120. [PMID: 37126718 PMCID: PMC10175843 DOI: 10.1073/pnas.2219469120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/21/2023] [Indexed: 05/03/2023] Open
Abstract
Basic helix-loop-helix (bHLH) proteins are one of the largest families of transcription factor (TF) in eukaryotes, and ~30% of all flowering plants' bHLH TFs contain the aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain at variable distances C-terminal from the bHLH. However, the evolutionary history and functional consequences of the bHLH/ACT-like domain association remain unknown. Here, we show that this domain association is unique to the plantae kingdom with green algae (chlorophytes) harboring a small number of bHLH genes with variable frequency of ACT-like domain's presence. bHLH-associated ACT-like domains form a monophyletic group, indicating a common origin. Indeed, phylogenetic analysis results suggest that the association of ACT-like and bHLH domains occurred early in Plantae by recruitment of an ACT-like domain in a common ancestor with widely distributed ACT DOMAIN REPEAT (ACR) genes by an ancestral bHLH gene. We determined the functional significance of this association by showing that Chlamydomonas reinhardtii ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. We show that, while ACT-like domains have experienced faster selection than the associated bHLH domain, their rates of evolution are strongly and positively correlated, suggesting that the evolution of the ACT-like domains was constrained by the bHLH domains. This study proposes an evolutionary trajectory for the association of ACT-like and bHLH domains with the experimental characterization of the functional consequence in the regulation of plant-specific processes, highlighting the impacts of functional domain coevolution.
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Affiliation(s)
- Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI48824
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI48824
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI48824
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Li P, Chen L, Gu X, Zhao M, Wang W, Hou S. FOUR LIPS plays a role in meristemoid-to-GMC fate transition during stomatal development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:424-436. [PMID: 36786686 DOI: 10.1111/tpj.16146] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/07/2023] [Indexed: 05/10/2023]
Abstract
Meristemoids, which are stomatal precursor cells, exhibit self-renewal and differentiation abilities. However, the only known core factor associated with meristemoid division termination and fate transition is the heterodimer formed by the basic helix-loop-helix proteins MUTE and SCREAMs (SCRMs). FOUR LIPS (FLP), a well-known transcription factor that restricts guard mother cell (GMC) division, is a direct target of MUTE. Whether FLP involves in meristemoid differentiation is unknown. Through sensitized genetic screening of flp-1, we identified a mute-like (mutl) mutant with arrested meristemoids. The mutant carried a novel allele of the MUTE locus, i.e., mute-4. Intriguingly, mute-4 is a hypomorphic allele that exhibits wild-type appearance with slightly delayed meristemoid-to-GMC transition, whereas it renders an unexpected mutl epidermis with most meristemoids arrested and very few stomata when combined with flp (flp mute-4), suggesting that FLP is a positive regulator during this transition process. Consistently, the expression of FLP increased during GMC commitment, and the number of cells at this stage was markedly increased in flp. flp scrm double mutants produced arrested meristemoids similar to mute, and FLP was able to interact physically with SCRM. Taken together, our results demonstrate that FLP functions together with MUTE and SCRMs to direct meristemoid-to-GMC fate transition.
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Affiliation(s)
- Ping Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Liang Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoli Gu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Mingfeng Zhao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wenjin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Suiwen Hou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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8
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Alsamman AM, Abdelsattar M, El Allali A, Radwan KH, Nassar AE, Mousa KH, Hussein A, Mokhtar MM, Abd El-Maksoud MM, Istanbuli T, Kehel Z, Hamwieh A. Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea. Front Genet 2023; 14:1128992. [PMID: 37021003 PMCID: PMC10067732 DOI: 10.3389/fgene.2023.1128992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/02/2023] [Indexed: 03/22/2023] Open
Abstract
Background: The basic helix-loop-helix (bHLH) transcription factor is a vital component in plant biology, with a significant impact on various aspects of plant growth, cell development, and physiological processes. Grass pea is a vital agricultural crop that plays a crucial role in food security. However, the lack of genomic information presents a major challenge to its improvement and development. This highlights the urgency for deeper investigation into the function of bHLH genes in grass pea to improve our understanding of this important crop.Results: The identification of bHLH genes in grass pea was performed on a genome-wide scale using genomic and transcriptomic screening. A total of 122 genes were identified as having conserved bHLH domains and were functionally and fully annotated. The LsbHLH proteins could be classified into 18 subfamilies. There were variations in intron-exon distribution, with some genes lacking introns. The cis-element and gene enrichment analyses showed that the LsbHLHs were involved in various plant functions, including response to phytohormones, flower and fruit development, and anthocyanin synthesis. A total of 28 LsbHLHs were found to have cis-elements associated with light response and endosperm expression biosynthesis. Ten conserved motifs were identified across the LsbHLH proteins. The protein-protein interaction analysis showed that all LsbHLH proteins interacted with each other, and nine of them displayed high levels of interaction. RNA-seq analysis of four Sequence Read Archive (SRA) experiments showed high expression levels of LsbHLHs across a range of environmental conditions. Seven highly expressed genes were selected for qPCR validation, and their expression patterns in response to salt stress showed that LsbHLHD4, LsbHLHD5, LsbHLHR6, LsbHLHD8, LsbHLHR14, LsbHLHR68, and LsbHLHR86 were all expressed in response to salt stress.Conclusion: The study provides an overview of the bHLH family in the grass pea genome and sheds light on the molecular mechanisms underlying the growth and evolution of this crop. The report covers the diversity in gene structure, expression patterns, and potential roles in regulating plant growth and response to environmental stress factors in grass pea. The identified candidate LsbHLHs could be utilized as a tool to enhance the resilience and adaptation of grass pea to environmental stress.
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Affiliation(s)
- Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- *Correspondence: Achraf El Allali, ; Aladdin Hamwieh,
| | - Khaled H. Radwan
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- National Biotechnology Network of Expertise, ASRT, Cairo, Egypt
| | - Ahmed E. Nassar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled H. Mousa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | | | - Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
- *Correspondence: Achraf El Allali, ; Aladdin Hamwieh,
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9
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McKown KH, Anleu Gil MX, Mair A, Xu SL, Raissig MT, Bergmann DC. Expanded roles and divergent regulation of FAMA in Brachypodium and Arabidopsis stomatal development. THE PLANT CELL 2023; 35:756-775. [PMID: 36440974 PMCID: PMC9940870 DOI: 10.1093/plcell/koac341] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/29/2022] [Accepted: 11/24/2022] [Indexed: 05/07/2023]
Abstract
Stomata, cellular valves found on the surfaces of aerial plant tissues, present a paradigm for studying cell fate and patterning in plants. A highly conserved core set of related basic helix-loop-helix (bHLH) transcription factors regulates stomatal development across diverse species. We characterized BdFAMA in the temperate grass Brachypodium distachyon and found this late-acting transcription factor was necessary and sufficient for specifying stomatal guard cell fate, and unexpectedly, could also induce the recruitment of subsidiary cells in the absence of its paralogue, BdMUTE. The overlap in function is paralleled by an overlap in expression pattern and by unique regulatory relationships between BdMUTE and BdFAMA. To better appreciate the relationships among the Brachypodium stomatal bHLHs, we used in vivo proteomics in developing leaves and found evidence for multiple shared interaction partners. We reexamined the roles of these genes in Arabidopsis thaliana by testing genetic sufficiency within and across species, and found that while BdFAMA and AtFAMA can rescue stomatal production in Arabidopsis fama and mute mutants, only AtFAMA can specify Brassica-specific myrosin idioblasts. Taken together, our findings refine the current models of stomatal bHLH function and regulatory feedback among paralogues within grasses as well as across the monocot/dicot divide.
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Affiliation(s)
- Katelyn H McKown
- Department of Genetics, Stanford School of Medicine, Stanford, California 94305, USA
| | - M Ximena Anleu Gil
- Biology Department, Stanford University, 371 Jane Stanford Way, Stanford, California 94305, USA
| | - Andrea Mair
- Biology Department, Stanford University, 371 Jane Stanford Way, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University, 371 Jane Stanford Way, Stanford, California 94305, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama St., Stanford, California 94305, USA
| | - Michael T Raissig
- Biology Department, Stanford University, 371 Jane Stanford Way, Stanford, California 94305, USA
| | - Dominique C Bergmann
- Biology Department, Stanford University, 371 Jane Stanford Way, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University, 371 Jane Stanford Way, Stanford, California 94305, USA
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10
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Moriya KC, Shirakawa M, Loue-Manifel J, Matsuda Y, Lu YT, Tamura K, Oka Y, Matsushita T, Hara-Nishimura I, Ingram G, Nishihama R, Goodrich J, Kohchi T, Shimada T. Stomatal regulators are co-opted for seta development in the astomatous liverwort Marchantia polymorpha. NATURE PLANTS 2023; 9:302-314. [PMID: 36658391 DOI: 10.1038/s41477-022-01325-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The evolution of special types of cells requires the acquisition of new gene regulatory networks controlled by transcription factors (TFs). In stomatous plants, a TF module formed by subfamilies Ia and IIIb basic helix-loop-helix TFs (Ia-IIIb bHLH) regulates stomatal formation; however, how this module evolved during land plant diversification remains unclear. Here we show that, in the astomatous liverwort Marchantia polymorpha, a Ia-IIIb bHLH module regulates the development of a unique sporophyte tissue, the seta, which is found in mosses and liverworts. The sole Ia bHLH gene, MpSETA, and a IIIb bHLH gene, MpICE2, regulate the cell division and/or differentiation of seta lineage cells. MpSETA can partially replace the stomatal function of Ia bHLH TFs in Arabidopsis thaliana, suggesting that a common regulatory mechanism underlies setal and stomatal formation. Our findings reveal the co-option of a Ia-IIIb bHLH TF module for regulating cell fate determination and/or cell division of distinct types of cells during land plant evolution.
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Affiliation(s)
- Kenta C Moriya
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Makoto Shirakawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Jeanne Loue-Manifel
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, CNRS, INRAE, UCB Lyon 1, Lyon, France
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, UK
| | - Yoriko Matsuda
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yen-Ting Lu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, UK
| | - Kentaro Tamura
- School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yoshito Oka
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | | | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, CNRS, INRAE, UCB Lyon 1, Lyon, France
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Justin Goodrich
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, UK
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tomoo Shimada
- Graduate School of Science, Kyoto University, Kyoto, Japan.
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11
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Kim ED, Dorrity MW, Fitzgerald BA, Seo H, Sepuru KM, Queitsch C, Mitsuda N, Han SK, Torii KU. Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment. NATURE PLANTS 2022; 8:1453-1466. [PMID: 36522450 PMCID: PMC9788986 DOI: 10.1038/s41477-022-01304-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/28/2022] [Indexed: 05/12/2023]
Abstract
Chromatin architecture and transcription factor (TF) binding underpin cell-fate specification during development, but their mutual regulatory relationships remain unclear. Here we report an atlas of dynamic chromatin landscapes during stomatal cell-lineage progression, in which sequential cell-state transitions are governed by lineage-specific bHLH TFs. Major reprogramming of chromatin accessibility occurs at the proliferation-to-differentiation transition. We discover novel co-cis regulatory elements (CREs) signifying the early precursor stage, BBR/BPC (GAGA) and bHLH (E-box) motifs, where master-regulatory bHLH TFs, SPEECHLESS and MUTE, consecutively bind to initiate and terminate the proliferative state, respectively. BPC TFs complex with MUTE to repress SPEECHLESS expression through a local deposition of repressive histone marks. We elucidate the mechanism by which cell-state-specific heterotypic TF complexes facilitate cell-fate commitment by recruiting chromatin modifiers via key co-CREs.
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Affiliation(s)
- Eun-Deok Kim
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bridget A Fitzgerald
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hyemin Seo
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Krishna Mohan Sepuru
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Soon-Ki Han
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan.
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