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Gautrat P, Buti S, Romanowski A, Lammers M, Matton SEA, Buijs G, Pierik R. Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues. Nat Commun 2024; 15:8489. [PMID: 39353942 PMCID: PMC11445486 DOI: 10.1038/s41467-024-52828-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 09/23/2024] [Indexed: 10/03/2024] Open
Abstract
Plants growing at high densities can detect competitors through changes in the composition of light reflected by neighbours. In response to this far-red-enriched light, plants elicit adaptive shade avoidance responses for light capture, but these need to be balanced against other input signals, such as nutrient availability. Here, we investigated how Arabidopsis integrates shade and nitrate signalling. We unveiled that nitrate modulates shade avoidance via a previously unknown shade response pathway that involves root-derived trans-zeatin (tZ) signal and the BEE1 transcription factor as an integrator of light and cytokinin signalling. Under nitrate-sufficient conditions, tZ promotes hypocotyl elongation specifically in the presence of supplemental far-red light. This occurs via PIF transcription factors-dependent inhibition of type-A ARRs cytokinin response inhibitors. Our data thus reveal how plants co-regulate responses to shade cues with root-derived information about nutrient availability, and how they restrict responses to this information to specific light conditions in the shoot.
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Affiliation(s)
- Pierre Gautrat
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
| | - Sara Buti
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Andrés Romanowski
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Michiel Lammers
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Sanne E A Matton
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands
| | - Guido Buijs
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Ronald Pierik
- Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
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2
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Lopes FL, Formosa-Jordan P, Malivert A, Margalha L, Confraria A, Feil R, Lunn JE, Jönsson H, Landrein B, Baena-González E. Sugar signaling modulates SHOOT MERISTEMLESS expression and meristem function in Arabidopsis. Proc Natl Acad Sci U S A 2024; 121:e2408699121. [PMID: 39240964 PMCID: PMC11406306 DOI: 10.1073/pnas.2408699121] [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: 05/07/2024] [Accepted: 07/25/2024] [Indexed: 09/08/2024] Open
Abstract
In plants, development of all above-ground tissues relies on the shoot apical meristem (SAM) which balances cell proliferation and differentiation to allow life-long growth. To maximize fitness and survival, meristem activity is adjusted to the prevailing conditions through a poorly understood integration of developmental signals with environmental and nutritional information. Here, we show that sugar signals influence SAM function by altering the protein levels of SHOOT MERISTEMLESS (STM), a key regulator of meristem maintenance. STM is less abundant in inflorescence meristems with lower sugar content, resulting from plants being grown or treated under limiting light conditions. Additionally, sucrose but not light is sufficient to sustain STM accumulation in excised inflorescences. Plants overexpressing the α1-subunit of SUCROSE-NON-FERMENTING1-RELATED KINASE 1 (SnRK1) accumulate less STM protein under optimal light conditions, despite higher sugar accumulation in the meristem. Furthermore, SnRK1α1 interacts physically with STM and inhibits its activity in reporter assays, suggesting that SnRK1 represses STM protein function. Contrasting the absence of growth defects in SnRK1α1 overexpressors, silencing SnRK1α in the SAM leads to meristem dysfunction and severe developmental phenotypes. This is accompanied by reduced STM transcript levels, suggesting indirect effects on STM. Altogether, we demonstrate that sugars promote STM accumulation and that the SnRK1 sugar sensor plays a dual role in the SAM, limiting STM function under unfavorable conditions but being required for overall meristem organization and integrity under favorable conditions. This highlights the importance of sugars and SnRK1 signaling for the proper coordination of meristem activities.
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Affiliation(s)
- Filipa L Lopes
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Pau Formosa-Jordan
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Max Planck Institute for Plant Breeding Research, Cologne D-50829, Germany
| | - Alice Malivert
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut National de la Recherche Agronomique, Lyon Cedex 07 69342, France
| | - Leonor Margalha
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Ana Confraria
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Henrik Jönsson
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0DZ, United Kingdom
- Computational Biology and Biological Physics, Lund University, Lund 223 62, Sweden
| | - Benoît Landrein
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut National de la Recherche Agronomique, Lyon Cedex 07 69342, France
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
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3
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Tessi TM, Maurino VG. AZGs: a new family of cytokinin transporters. Biochem Soc Trans 2024; 52:1841-1848. [PMID: 38979638 DOI: 10.1042/bst20231537] [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: 04/26/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/10/2024]
Abstract
Cytokinins (CKs) are phytohormones structurally similar to purines that play important roles in various aspects of plant physiology and development. The local and long-distance distribution of CKs is very important to control their action throughout the plant body. Over the past decade, several novel CK transporters have been described, many of which have been linked to a physiological function rather than simply their ability to transport the hormone in vitro. Purine permeases, equilibrative nucleotide transporters and ATP-binding cassette transporters are involved in the local and long-range distribution of CK. In addition, members of the Arabidopsis AZA-GUANINE RESISTANT (AZG) protein family, AZG1 and AZG2, have recently been shown to mediate CK uptake at the plasma membrane and endoplasmic reticulum. Despite sharing ∼50% homology, AZG1 and AZG2 have unique transport mechanisms, tissue-specific expression patterns, and subcellular localizations that underlie their distinct physiological functions. AZG2 is expressed in a small group of cells in the overlying tissue around the lateral root primordia, where its expression is induced by auxins and it is involved in the regulation of lateral root growth. AZG1 is ubiquitously expressed, with high levels in the division zone of the root apical meristem. Here, it binds and stabilises the auxin efflux carrier PIN1, thereby shaping root architecture, particularly under salt stress. This review highlights the latest findings on the protein properties, transport mechanisms and cellular functions of this new family of CK transporters and discusses perspectives for future research in this field.
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Affiliation(s)
- Tomas M Tessi
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg 69120, Germany
| | - Veronica G Maurino
- Molecular Plant Physiology, Institute of Cellular Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
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4
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Dziewit K, Amakorová P, Novák O, Szal B, Podgórska A. Systemic strategies for cytokinin biosynthesis and catabolism in Arabidopsis roots and leaves under prolonged ammonium nutrition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108858. [PMID: 38924907 DOI: 10.1016/j.plaphy.2024.108858] [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: 11/09/2023] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
Cytokinins are growth-regulating plant hormones that are considered to adjust plant development under environmental stresses. During sole ammonium nutrition, a condition known to induce growth retardation of plants, altered cytokinin content can contribute to the characteristic ammonium toxicity syndrome. To understand the metabolic changes in cytokinin pools, cytokinin biosynthesis and degradation were analyzed in the leaves and roots of mature Arabidopsis plants. We found that in leaves of ammonium-grown plants, despite induction of biosynthesis on the expression level, there was no active cytokinin build-up because they were effectively routed toward their downstream catabolites. In roots, cytokinin conjugation was also induced, together with low expression of major synthetic enzymes, resulting in a decreased content of the trans-zeatin form under ammonium conditions. Based on these results, we hypothesized that in leaves and roots, cytokinin turnover is the major regulator of the cytokinin pool and does not allow active cytokinins to accumulate. A potent negative-regulator of root development is trans-zeatin, therefore its low level in mature root tissues of ammonium-grown plants may be responsible for occurrence of a wide root system. Additionally, specific cytokinin enhancement in apical root tips may evoke a short root phenotype in plants under ammonium conditions. The ability to flexibly regulate cytokinin metabolism and distribution in root and shoot tissues can contribute to adjusting plant development in response to ammonium stress.
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Affiliation(s)
- Kacper Dziewit
- Department of Plant Bioenergetics, Faculty of Biology, University of Warsaw, I. Miecznikowa 01, 02-096, Warsaw, Poland.
| | - Petra Amakorová
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic.
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic.
| | - Bożena Szal
- Department of Plant Bioenergetics, Faculty of Biology, University of Warsaw, I. Miecznikowa 01, 02-096, Warsaw, Poland.
| | - Anna Podgórska
- Department of Plant Bioenergetics, Faculty of Biology, University of Warsaw, I. Miecznikowa 01, 02-096, Warsaw, Poland.
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5
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Soyano T, Akamatsu A, Takeda N, Watahiki MK, Goh T, Okuma N, Suganuma N, Kojima M, Takebayashi Y, Sakakibara H, Nakajima K, Kawaguchi M. Periodic cytokinin responses in Lotus japonicus rhizobium infection and nodule development. Science 2024; 385:288-294. [PMID: 39024445 DOI: 10.1126/science.adk5589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 04/26/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Host plants benefit from legume root nodule symbiosis with nitrogen-fixing bacteria under nitrogen-limiting conditions. In this interaction, the hosts must regulate nodule numbers and distribution patterns to control the degree of symbiosis and maintain root growth functions. The host response to symbiotic bacteria occurs discontinuously but repeatedly at the region behind the tip of the growing roots. Here, live-imaging and transcriptome analyses revealed oscillating host gene expression with approximately 6-hour intervals upon bacterial inoculation. Cytokinin response also exhibited a similar oscillation pattern. Cytokinin signaling is crucial to maintaining the periodicity, as observed in cytokinin receptor mutants displaying altered infection foci distribution. This periodic regulation influences the size of the root region responsive to bacteria, as well as the nodulation process progression.
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Affiliation(s)
- Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Basic Biology Program, Graduate University for Advanced Studies, SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Akira Akamatsu
- Graduate School of Biological and Environmental Sciences, Kwansei Gakuin University, Gakuen Uegahara 1, Sanda, Hyogo 669-1330, Japan
| | - Naoya Takeda
- Graduate School of Biological and Environmental Sciences, Kwansei Gakuin University, Gakuen Uegahara 1, Sanda, Hyogo 669-1330, Japan
| | - Masaaki K Watahiki
- Faculty of Science, Division of Biological Sciences, Hokkaido University, Kitaku Kita 10, Nishi 8, Sapporo 060-0810, Japan
| | - Tatsuaki Goh
- Nara Institute of Science and Technology, Graduate School of Science and Technology, Division of Biological Science, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Nao Okuma
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Norio Suganuma
- Department of Life Science, Aichi University of Education, Kariya, Aichi 448-8542, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Keiji Nakajima
- Nara Institute of Science and Technology, Graduate School of Science and Technology, Division of Biological Science, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Basic Biology Program, Graduate University for Advanced Studies, SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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6
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Damodaran S, Strader LC. Factors governing cellular reprogramming competence in Arabidopsis adventitious root formation. Dev Cell 2024:S1534-5807(24)00397-6. [PMID: 39043189 DOI: 10.1016/j.devcel.2024.06.019] [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: 03/12/2023] [Revised: 02/25/2024] [Accepted: 06/25/2024] [Indexed: 07/25/2024]
Abstract
Developmental reprogramming allows for flexibility in growth and adaptation to changing environmental conditions. In plants, wounding events can result in new stem cell niches and lateral organs. Adventitious roots develop from aerial parts of the plant and are regulated by multiple stimuli, including wounding. Here, we find that Arabidopsis thaliana seedlings wounded at the hypocotyl-root junction reprogram certain pericycle cells to produce adventitious roots proximal to the wound site. We have determined that competence for this reprogramming is controlled; basal cells close to the wound site can produce adventitious roots, whereas cells distal from the wound site mostly cannot. We found that altering cytokinin response or indole-3-butyric acid (IBA)-to-(indole-3-acetic acid) IAA conversion resulted in an expanded adventitious root competence zone and delineated the connection between these pathways. Our work highlights the importance of endogenous IBA-derived auxin and its interaction with cytokinin in adventitious root formation and the regenerative properties of plants.
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Affiliation(s)
- Suresh Damodaran
- Department of Biology, Duke University, Durham, NC 27708, USA; Duke Center for Quantitative BioDesign, Durham, NC 27708, USA
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27708, USA; Duke Center for Quantitative BioDesign, Durham, NC 27708, USA.
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7
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Zhao J, Wang J, Liu J, Zhang P, Kudoyarova G, Liu CJ, Zhang K. Spatially distributed cytokinins: Metabolism, signaling, and transport. PLANT COMMUNICATIONS 2024; 5:100936. [PMID: 38689499 PMCID: PMC11287186 DOI: 10.1016/j.xplc.2024.100936] [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: 10/30/2023] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/02/2024]
Abstract
Cytokinins are mobile phytohormones that regulate plant growth, development, and environmental adaptability. The major cytokinin species include isopentenyl adenine (iP), trans-zeatin (tZ), cis-zeatin (cZ), and dihydrozeatin (DZ). The spatial distributions of different cytokinin species in different organelles, cells, tissues, and organs are primarily shaped by biosynthesis via isopentenyltransferases (IPT), cytochrome P450 monooxygenase, and 5'-ribonucleotide phosphohydrolase and by conjugation or catabolism via glycosyltransferase or cytokinin oxidase/dehydrogenase. Cytokinins bind to histidine receptor kinases in the endoplasmic reticulum or plasma membrane and relay signals to response regulators in the nucleus via shuttle proteins known as histidine phosphotransfer proteins. The movements of cytokinins from sites of biosynthesis to sites of signal perception usually require long-distance, intercellular, and intracellular transport. In the past decade, ATP-binding cassette (ABC) transporters, purine permeases (PUP), AZA-GUANINE RESISTANT (AZG) transporters, equilibrative nucleoside transporters (ENT), and Sugars Will Eventually Be Exported transporters (SWEET) have been characterized as involved in cytokinin transport processes. This review begins by introducing the spatial distributions of various cytokinins and the subcellular localizations of the proteins involved in their metabolism and signaling. Highlights focus on an inventory of the characterized transporters involved in cytokinin compartmentalization, including long-distance, intercellular, and intracellular transport, and the regulation of the spatial distributions of cytokinins by environmental cues. Future directions for cytokinin research are also discussed.
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Affiliation(s)
- Jiangzhe Zhao
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Jingqi Wang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Jie Liu
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Penghong Zhang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Guzel Kudoyarova
- Ufa Institute of Biology, Ufa Federal Research Center, RAS, Prospekt Oktyabrya 69, Ufa 450054, Russia
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kewei Zhang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China.
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8
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Moore S, Jervis G, Topping JF, Chen C, Liu J, Lindsey K. A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root. PLANT COMMUNICATIONS 2024; 5:100886. [PMID: 38504522 PMCID: PMC11287175 DOI: 10.1016/j.xplc.2024.100886] [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: 10/10/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/21/2024]
Abstract
The interaction between auxin and cytokinin is important in many aspects of plant development. Experimental measurements of both auxin and cytokinin concentration and reporter gene expression clearly show the coexistence of auxin and cytokinin concentration patterning in Arabidopsis root development. However, in the context of crosstalk among auxin, cytokinin, and ethylene, little is known about how auxin and cytokinin concentration patterns simultaneously emerge and how they regulate each other in the Arabidopsis root. This work utilizes a wide range of experimental observations to propose a mechanism for simultaneous patterning of auxin and cytokinin concentrations. In addition to revealing the regulatory relationships between auxin and cytokinin, this mechanism shows that ethylene signaling is an important factor in achieving simultaneous auxin and cytokinin patterning, while also predicting other experimental observations. Combining the mechanism with a realistic in silico root model reproduces experimental observations of both auxin and cytokinin patterning. Predictions made by the mechanism can be compared with a variety of experimental observations, including those obtained by our group and other independent experiments reported by other groups. Examples of these predictions include patterning of auxin biosynthesis rate, changes in PIN1 and PIN2 patterns in pin3,4,7 mutants, changes in cytokinin patterning in the pls mutant, PLS patterning, and various trends in different mutants. This research reveals a plausible mechanism for simultaneous patterning of auxin and cytokinin concentrations in Arabidopsis root development and suggests a key role for ethylene pattern integration.
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Affiliation(s)
- Simon Moore
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - George Jervis
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Jennifer F Topping
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Chunli Chen
- Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junli Liu
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK.
| | - Keith Lindsey
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK.
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9
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Fernandez‐Moreno J, Yaschenko AE, Neubauer M, Marchi AJ, Zhao C, Ascencio‐Ibanez JT, Alonso JM, Stepanova AN. A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1942-1956. [PMID: 38379432 PMCID: PMC11182585 DOI: 10.1111/pbi.14313] [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: 12/21/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Advancement of DNA-synthesis technologies has greatly facilitated the development of synthetic biology tools. However, high-complexity DNA sequences containing tandems of short repeats are still notoriously difficult to produce synthetically, with commercial DNA synthesis companies usually rejecting orders that exceed specific sequence complexity thresholds. To overcome this limitation, we developed a simple, single-tube reaction method that enables the generation of DNA sequences containing multiple repetitive elements. Our strategy involves commercial synthesis and PCR amplification of padded sequences that contain the repeats of interest, along with random intervening sequence stuffers that include type IIS restriction enzyme sites. GoldenBraid molecular cloning technology is then employed to remove the stuffers, rejoin the repeats together in a predefined order, and subclone the tandem(s) in a vector using a single-tube digestion-ligation reaction. In our hands, this new approach is much simpler, more versatile and efficient than previously developed solutions to this problem. As a proof of concept, two different phytohormone-responsive, synthetic, repetitive proximal promoters were generated and tested in planta in the context of transcriptional reporters. Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes. These encouraging results suggest that this reporter system can be leveraged to investigate the ethylene response to biotic and abiotic factors with high spatial and temporal resolution.
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Affiliation(s)
| | - Anna E. Yaschenko
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Matthew Neubauer
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Alex J. Marchi
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Chengsong Zhao
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - José T. Ascencio‐Ibanez
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Jose M. Alonso
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Anna N. Stepanova
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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10
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Zhang Y, Duan X, Wang Z, Lv Y, Qi W, Li L, Luo L, Xuan W. CEPs suppress auxin signaling but promote cytokinin signaling to inhibit root growth in Arabidopsis. Biochem Biophys Res Commun 2024; 711:149934. [PMID: 38626621 DOI: 10.1016/j.bbrc.2024.149934] [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: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/18/2024]
Abstract
C-terminally encoded peptides (CEPs) are peptide hormones that function as mobile signals coordinating crucial developmental programs in plants. Previous studies have revealed that CEPs exert negative regulation on root development through interaction with CEP receptors (CEPRs), CEP DOWNSTREAMs (CEPDs), the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE (AHKs) and the transcriptional repressor Auxin/Indole-3-Acetic Acid (AUX/IAA). However, the precise molecular mechanisms underlying CEPs-mediated regulation of root development via auxin and cytokinin signaling pathways still necessitate further detailed investigation. In this study, we examined prior research and elucidated the underlying molecular mechanisms. The results showed that both synthetic AtCEPs and overexpression of AtCEP5 markedly supressed primary root elongation and lateral root (LR) formation in Arabidopsis. Molecular biology and genetics elucidated how CEPs inhibit root growth by suppressing auxin signaling while promoting cytokinin signaling. In summary, this study elucidated the inhibitory effects of AtCEPs on Arabidopsis root growth and provided insights into their potential molecular mechanisms, thus enhancing our comprehension of CEP-mediated regulation of plant growth and development.
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Affiliation(s)
- Yuwen Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xingliang Duan
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanda Lv
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China; Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Weicong Qi
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China; Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Lun Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Le Luo
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Xuan
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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11
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García-Gómez ML, Ten Tusscher K. Multi-scale mechanisms driving root regeneration: From regeneration competence to tissue repatterning. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38824611 DOI: 10.1111/tpj.16860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024]
Abstract
Plants possess an outstanding capacity to regenerate enabling them to repair damages caused by suboptimal environmental conditions, biotic attacks, or mechanical damages impacting the survival of these sessile organisms. Although the extent of regeneration varies greatly between localized cell damage and whole organ recovery, the process of regeneration can be subdivided into a similar sequence of interlinked regulatory processes. That is, competence to regenerate, cell fate reprogramming, and the repatterning of the tissue. Here, using root tip regeneration as a paradigm system to study plant regeneration, we provide a synthesis of the molecular responses that underlie both regeneration competence and the repatterning of the root stump. Regarding regeneration competence, we discuss the role of wound signaling, hormone responses and synthesis, and rapid changes in gene expression observed in the cells close to the cut. Then, we consider how this rapid response is followed by the tissue repatterning phase, where cells experience cell fate changes in a spatial and temporal order to recreate the lost stem cell niche and columella. Lastly, we argue that a multi-scale modeling approach is fundamental to uncovering the mechanisms underlying root regeneration, as it allows to integrate knowledge of cell-level gene expression, cell-to-cell transport of hormones and transcription factors, and tissue-level growth dynamics to reveal how the bi-directional feedbacks between these processes enable self-organized repatterning of the root apex.
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Affiliation(s)
- Monica L García-Gómez
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Experimental and Computational Plant Development Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- CropXR Institute, Utrecht, The Netherlands
- Translational Plant Biology Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Kirsten Ten Tusscher
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Experimental and Computational Plant Development Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- CropXR Institute, Utrecht, The Netherlands
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12
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Argueso CT, Kieber JJ. Cytokinin: From autoclaved DNA to two-component signaling. THE PLANT CELL 2024; 36:1429-1450. [PMID: 38163638 PMCID: PMC11062471 DOI: 10.1093/plcell/koad327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 01/03/2024]
Abstract
Since its first identification in the 1950s as a regulator of cell division, cytokinin has been linked to many physiological processes in plants, spanning growth and development and various responses to the environment. Studies from the last two and one-half decades have revealed the pathways underlying the biosynthesis and metabolism of cytokinin and have elucidated the mechanisms of its perception and signaling, which reflects an ancient signaling system evolved from two-component elements in bacteria. Mutants in the genes encoding elements involved in these processes have helped refine our understanding of cytokinin functions in plants. Further, recent advances have provided insight into the mechanisms of intracellular and long-distance cytokinin transport and the identification of several proteins that operate downstream of cytokinin signaling. Here, we review these processes through a historical lens, providing an overview of cytokinin metabolism, transport, signaling, and functions in higher plants.
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Affiliation(s)
- Cristiana T Argueso
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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13
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El Arbi N, Schürholz AK, Handl MU, Schiffner A, Hidalgo Prados I, Schnurbusch L, Wenzl C, Zhao X, Zeng J, Lohmann JU, Wolf S. ARGONAUTE10 controls cell fate specification and formative cell divisions in the Arabidopsis root. EMBO J 2024; 43:1822-1842. [PMID: 38565947 PMCID: PMC11066080 DOI: 10.1038/s44318-024-00072-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
A key question in plant biology is how oriented cell divisions are integrated with patterning mechanisms to generate organs with adequate cell type allocation. In the root vasculature, a gradient of miRNA165/6 controls the abundance of HD-ZIP III transcription factors, which in turn control cell fate and spatially restrict vascular cell proliferation to specific cells. Here, we show that vascular development requires the presence of ARGONAUTE10, which is thought to sequester miRNA165/6 and protect HD-ZIP III transcripts from degradation. Our results suggest that the miR165/6-AGO10-HDZIP III module acts by buffering cytokinin responses and restricting xylem differentiation. Mutants of AGO10 show faster growth rates and strongly enhanced survival under severe drought conditions. However, this superior performance is offset by markedly increased variation and phenotypic plasticity in sub-optimal carbon supply conditions. Thus, AGO10 is required for the control of formative cell division and coordination of robust cell fate specification of the vasculature, while altering its expression provides a means to adjust phenotypic plasticity.
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Affiliation(s)
- Nabila El Arbi
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Department of Plant Physiology, Umea Plant Science Centre, Umea, Sweden
| | - Ann-Kathrin Schürholz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Corden Pharma, Heidelberg, Germany
| | - Marlene U Handl
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Alexei Schiffner
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Inés Hidalgo Prados
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Liese Schnurbusch
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Christian Wenzl
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Xin'Ai Zhao
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jian Zeng
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jan U Lohmann
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Sebastian Wolf
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany.
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14
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Henry AR, Miller ND, Spalding EP. QTL for the Kinematic Traits That Define the Arabidopsis Root Elongation Zone and Their Relationship to Gravitropism. PLANTS (BASEL, SWITZERLAND) 2024; 13:1189. [PMID: 38732404 PMCID: PMC11085590 DOI: 10.3390/plants13091189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Cell expansion in a discrete region called the elongation zone drives root elongation. Analyzing time lapse images can quantify the expansion in kinematic terms as if it were fluid flow. We used horizontal microscopes to collect images from which custom software extracted the length of the elongation zone, the peak relative elemental growth rate (REGR) within it, the axial position of the REGR peak, and the root elongation rate. Automation enabled these kinematic traits to be measured in 1575 Arabidopsis seedlings representing 162 recombinant inbred lines (RILs) derived from a cross of Cvi and Ler ecotypes. We mapped ten quantitative trait loci (QTL), affecting the four kinematic traits. Three QTL affected two or more traits in these vertically oriented seedlings. We compared this genetic architecture with that previously determined for gravitropism using the same RIL population. The major QTL peaks for the kinematic traits did not overlap with the gravitropism QTL. Furthermore, no single kinematic trait correlated with quantitative descriptors of the gravitropism response curve across this population. In addition to mapping QTL for growth zone traits, this study showed that the size and shape of the elongation zone may vary widely without affecting the differential growth induced by gravity.
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Affiliation(s)
| | | | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA; (A.R.H.); (N.D.M.)
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15
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Velandia K, Correa-Lozano A, McGuiness PM, Reid JB, Foo E. Cell-layer specific roles for gibberellins in nodulation and root development. THE NEW PHYTOLOGIST 2024; 242:626-640. [PMID: 38396236 DOI: 10.1111/nph.19623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/01/2024] [Indexed: 02/25/2024]
Abstract
Gibberellins (GA) have a profound influence on the formation of lateral root organs. However, the precise role this hormone plays in the cell-specific events during lateral root formation, rhizobial infection and nodule organogenesis, including interactions with auxin and cytokinin (CK), is not clear. We performed epidermal- and endodermal-specific complementation of the severely GA-deficient na pea (Pisum sativum) mutant with Agrobacterium rhizogenes. Gibberellin mutants were used to examine the spatial expression pattern of CK (TCSn)- and auxin (DR5)-responsive promoters and hormone levels. We found that GA produced in the endodermis promote lateral root and nodule organogenesis and can induce a mobile signal(s) that suppresses rhizobial infection. By contrast, epidermal-derived GA suppress infection but have little influence on root or nodule development. GA suppress the CK-responsive TCSn promoter in the cortex and are required for normal auxin activation during nodule primordia formation. Our findings indicate that GA regulate the checkpoints between infection thread (IT) penetration of the cortex and invasion of nodule primordial cells and promote the subsequent progression of nodule development. It appears that GA limit the progression and branching of IT in the cortex by restricting CK response and activate auxin response to promote nodule primordia development.
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Affiliation(s)
- Karen Velandia
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Alejandro Correa-Lozano
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Peter M McGuiness
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - James B Reid
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Eloise Foo
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
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16
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Salvalaio M, Sena G. Long-term root electrotropism reveals habituation and hysteresis. PLANT PHYSIOLOGY 2024; 194:2697-2708. [PMID: 38156361 PMCID: PMC10980514 DOI: 10.1093/plphys/kiad686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/30/2023]
Abstract
Plant roots sense many physical and chemical cues in soil, such as gravity, humidity, light, and chemical gradients, and respond by redirecting their growth toward or away from the source of the stimulus. This process is called tropism. While gravitropism is the tendency to follow the gravitational field downwards, electrotropism is the alignment of growth with external electric fields and the induced ionic currents. Although root tropisms are at the core of their ability to explore large volumes of soil in search of water and nutrients, the molecular and physical mechanisms underlying most of them remain poorly understood. We have previously provided a quantitative characterization of root electrotropism in Arabidopsis (Arabidopsis thaliana) primary roots exposed for 5 h to weak electric fields, showing that auxin asymmetric distribution is not necessary for root electrotropism but that cytokinin biosynthesis is. Here, we extend that study showing that long-term electrotropism is characterized by a complex behavior. We describe overshoot and habituation as key traits of long-term root electrotropism in Arabidopsis and provide quantitative data about the role of past exposures in the response to electric fields (hysteresis). On the molecular side, we show that cytokinin, although necessary for root electrotropism, is not asymmetrically distributed during the bending. Overall, the data presented here represent a step forward toward a better understanding of the complexity of root behavior and provide a quantitative platform for future studies on the molecular mechanisms of electrotropism.
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Affiliation(s)
| | - Giovanni Sena
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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17
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He W, Truong HA, Zhang L, Cao M, Arakawa N, Xiao Y, Zhong K, Hou Y, Busch W. Identification of mebendazole as an ethylene signaling activator reveals a role of ethylene signaling in the regulation of lateral root angles. Cell Rep 2024; 43:113763. [PMID: 38358890 PMCID: PMC10949360 DOI: 10.1016/j.celrep.2024.113763] [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: 04/23/2022] [Revised: 08/31/2023] [Accepted: 01/24/2024] [Indexed: 02/17/2024] Open
Abstract
The lateral root angle or gravitropic set-point angle (GSA) is an important trait for root system architecture (RSA) that determines the radial expansion of the root system. The GSA therefore plays a crucial role for the ability of plants to access nutrients and water in the soil. Only a few regulatory pathways and mechanisms that determine GSA are known. These mostly relate to auxin and cytokinin pathways. Here, we report the identification of a small molecule, mebendazole (MBZ), that modulates GSA in Arabidopsis thaliana roots and acts via the activation of ethylene signaling. MBZ directly acts on the serine/threonine protein kinase CTR1, which is a negative regulator of ethylene signaling. Our study not only shows that the ethylene signaling pathway is essential for GSA regulation but also identifies a small molecular modulator of RSA that acts downstream of ethylene receptors and that directly activates ethylene signaling.
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Affiliation(s)
- Wenrong He
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Hai An Truong
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ling Zhang
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Min Cao
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Neal Arakawa
- Environmental and Complex Analysis Laboratory (ECAL), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kaizhen Zhong
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yingnan Hou
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, University of California, Riverside, Riverside, CA 92521, USA; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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18
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Ercoli MF, Shigenaga AM, de Araujo AT, Jain R, Ronald PC. Tyrosine-sulfated peptide hormone induces flavonol biosynthesis to control elongation and differentiation in Arabidopsis primary root. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578681. [PMID: 38352507 PMCID: PMC10862922 DOI: 10.1101/2024.02.02.578681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
In Arabidopsis roots, growth initiation and cessation are organized into distinct zones. How regulatory mechanisms are integrated to coordinate these processes and maintain proper growth progression over time is not well understood. Here, we demonstrate that the peptide hormone PLANT PEPTIDE CONTAINING SULFATED TYROSINE 1 (PSY1) promotes root growth by controlling cell elongation. Higher levels of PSY1 lead to longer differentiated cells with a shootward displacement of characteristics common to mature cells. PSY1 activates genes involved in the biosynthesis of flavonols, a group of plant-specific secondary metabolites. Using genetic and chemical approaches, we show that flavonols are required for PSY1 function. Flavonol accumulation downstream of PSY1 occurs in the differentiation zone, where PSY1 also reduces auxin and reactive oxygen species (ROS) activity. These findings support a model where PSY1 signals the developmental-specific accumulation of secondary metabolites to regulate the extent of cell elongation and the overall progression to maturation.
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Affiliation(s)
- Maria Florencia Ercoli
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Innovative Genomics Institute, University of California, Berkeley 94720
| | - Alexandra M Shigenaga
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Artur Teixeira de Araujo
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Joint Bioenergy Institute, Emeryville, California
| | - Rashmi Jain
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Innovative Genomics Institute, University of California, Berkeley 94720
- The Joint Bioenergy Institute, Emeryville, California
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19
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Marash I, Gupta R, Anand G, Leibman-Markus M, Lindner N, Israeli A, Nir D, Avni A, Bar M. TOR coordinates cytokinin and gibberellin signals mediating development and defense. PLANT, CELL & ENVIRONMENT 2024; 47:629-650. [PMID: 37904283 DOI: 10.1111/pce.14748] [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: 05/16/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023]
Abstract
Plants constantly perceive and process environmental signals and balance between the energetic demands of growth and defense. Growth arrest upon pathogen attack was previously suggested to result from a redirection of the plants' metabolic resources towards the activation of plant defense. The energy sensor Target of Rapamycin (TOR) kinase is a conserved master coordinator of growth and development in all eukaryotes. Although TOR is positioned at the interface between development and defense, little is known about the mechanisms by which TOR may potentially regulate the relationship between these two modalities. The plant hormones cytokinin (CK) and gibberellin (GA) execute various aspects of plant development and defense. The ratio between CK and GA was reported to determine the outcome of developmental programmes. Here, investigating the interplay between TOR-mediated development and TOR-mediated defense in tomato, we found that TOR silencing resulted in rescue of several different aberrant developmental phenotypes, demonstrating that TOR is required for the execution of developmental cues. In parallel, TOR inhibition enhanced immunity in genotypes with a low CK/GA ratio but not in genotypes with a high CK/GA ratio. TOR-inhibition mediated disease resistance was found to depend on developmental status, and was abolished in strongly morphogenetic leaves, while being strongest in mature, differentiated leaves. CK repressed TOR activity, suggesting that CK-mediated immunity may rely on TOR downregulation. At the same time, TOR activity was promoted by GA, and TOR silencing reduced GA sensitivity, indicating that GA signalling requires normal TOR activity. Our results demonstrate that TOR likely acts in concert with CK and GA signalling, executing signalling cues in both defense and development. Thus, differential regulation of TOR or TOR-mediated processes could regulate the required outcome of development-defense prioritisation.
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Affiliation(s)
- Iftah Marash
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan, Israel
- School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Rupali Gupta
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan, Israel
| | - Gautam Anand
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan, Israel
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan, Israel
| | - Naomi Lindner
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Israeli
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dov Nir
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Avni
- School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan, Israel
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20
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Chun Y, Fang J, Savelieva EM, Lomin SN, Shang J, Sun Y, Zhao J, Kumar A, Yuan S, Yao X, Liu CM, Arkhipov DV, Romanov GA, Li X. The cytokinin receptor OHK4/OsHK4 regulates inflorescence architecture in rice via an IDEAL PLANT ARCHITECTURE1/WEALTHY FARMER'S PANICLE-mediated positive feedback circuit. THE PLANT CELL 2023; 36:40-64. [PMID: 37811656 PMCID: PMC10734611 DOI: 10.1093/plcell/koad257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/07/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023]
Abstract
Inflorescence architecture is important for rice (Oryza sativa) grain yield. The phytohormone cytokinin (CK) has been shown to regulate rice inflorescence development; however, the underlying mechanism mediated by CK perception is still unclear. Employing a forward genetic approach, we isolated an inactive variant of the CK receptor OHK4/OsHK4 gene named panicle length1, which shows decreased panicle size due to reduced inflorescence meristem (IM) activity. A 2-amino acid deletion in the long α-helix stalk of the sensory module of OHK4 impairs the homodimerization and ligand-binding capacity of the receptor, even though the residues do not touch the ligand-binding domain or the dimerization interface. This deletion impairs CK signaling that occurs through the type-B response regulator OsRR21, which acts downstream of OHK4 in controlling inflorescence size. Meanwhile, we found that IDEAL PLANT ARCHITECTURE1(IPA1)/WEALTHY FARMER'S PANICLE (WFP), encoding a positive regulator of IM development, acts downstream of CK signaling and is directly activated by OsRR21. Additionally, we revealed that IPA1/WFP directly binds to the OHK4 promoter and upregulates its expression through interactions with 2 TCP transcription factors, forming a positive feedback circuit. Altogether, we identified the OHK4-OsRR21-IPA1 regulatory module, providing important insights into the role of CK signaling in regulating rice inflorescence architecture.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Xueyong Li
- Author for correspondence: (X.L.), (G.A.R.)
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21
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Azarova DS, Omelyanchuk NA, Mironova VV, Zemlyanskaya EV, Lavrekha VV. DyCeModel: a tool for 1D simulation for distribution of plant hormones controlling tissue patterning. Vavilovskii Zhurnal Genet Selektsii 2023; 27:890-897. [PMID: 38213710 PMCID: PMC10777285 DOI: 10.18699/vjgb-23-103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 01/13/2024] Open
Abstract
To study the mechanisms of growth and development, it is necessary to analyze the dynamics of the tissue patterning regulators in time and space and to take into account their effect on the cellular dynamics within a tissue. Plant hormones are the main regulators of the cell dynamics in plant tissues; they form gradients and maxima and control molecular processes in a concentration-dependent manner. Here, we present DyCeModel, a software tool implemented in MATLAB for one-dimensional simulation of tissue with a dynamic cellular ensemble, where changes in hormone (or other active substance) concentration in the cells are described by ordinary differential equations (ODEs). We applied DyCeModel to simulate cell dynamics in plant meristems with different cellular structures and demonstrated that DyCeModel helps to identify the relationships between hormone concentration and cellular behaviors. The tool visualizes the simulation progress and presents a video obtained during the calculation. Importantly, the tool is capable of automatically adjusting the parameters by fitting the distribution of the substance concentrations predicted in the model to experimental data taken from the microscopic images. Noteworthy, DyCeModel makes it possible to build models for distinct types of plant meristems with the same ODEs, recruiting specific input characteristics for each meristem. We demonstrate the tool's efficiency by simulation of the effect of auxin and cytokinin distributions on tissue patterning in two types of Arabidopsis thaliana stem cell niches: the root and shoot apical meristems. The resulting models represent a promising framework for further study of the role of hormone-controlled gene regulatory networks in cell dynamics.
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Affiliation(s)
- D S Azarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Omelyanchuk
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V V Mironova
- Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, the Netherlands
| | - E V Zemlyanskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V V Lavrekha
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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22
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Skalický V, Antoniadi I, Pěnčík A, Chamrád I, Lenobel R, Kubeš MF, Zatloukal M, Žukauskaitė A, Strnad M, Ljung K, Novák O. Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1825-1841. [PMID: 37682018 DOI: 10.1111/tpj.16456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023]
Abstract
Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.
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Affiliation(s)
- Vladimír Skalický
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Martin F Kubeš
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Marek Zatloukal
- Department of Chemical Biology, Faculty of Science, Palacký University, CZ-78371, Olomouc, Czech Republic
| | - Asta Žukauskaitė
- Department of Chemical Biology, Faculty of Science, Palacký University, CZ-78371, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
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23
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Leibman-Markus M, Schneider A, Gupta R, Marash I, Rav-David D, Carmeli-Weissberg M, Elad Y, Bar M. Immunity priming uncouples the growth-defense trade-off in tomato. Development 2023; 150:dev201158. [PMID: 37882831 DOI: 10.1242/dev.201158] [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: 07/25/2022] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
Plants have developed an array of mechanisms to protect themselves against pathogen invasion. The deployment of defense mechanisms is imperative for plant survival, but can come at the expense of plant growth, leading to the 'growth-defense trade-off' phenomenon. Following pathogen exposure, plants can develop resistance to further attack. This is known as induced resistance, or priming. Here, we investigated the growth-defense trade-off, examining how defense priming via systemic acquired resistance (SAR), or induced systemic resistance (ISR), affects tomato development and growth. We found that defense priming can promote, rather than inhibit, plant development, and that defense priming and growth trade-offs can be uncoupled. Cytokinin response was activated during induced resistance, and found to be required for the observed growth and disease resistance resulting from ISR activation. ISR was found to have a stronger effect than SAR on plant development. Our results suggest that growth promotion and induced resistance can be co-dependent, and that, in certain cases, defense priming can drive developmental processes and promote plant yield.
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Affiliation(s)
- Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Anat Schneider
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
- Department of Plant Pathology and Microbiology, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Rupali Gupta
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Iftah Marash
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
- School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Dalia Rav-David
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Mira Carmeli-Weissberg
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
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24
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Yan G, Li S, Ma M, Quan C, Tian X, Tu J, Shen J, Yi B, Fu T, Ma C, Guo L, Dai C. The transcription factor BnaWRKY10 regulates cytokinin dehydrogenase BnaCKX2 to control cytokinin distribution and seed size in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4994-5013. [PMID: 37246599 DOI: 10.1093/jxb/erad201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/25/2023] [Indexed: 05/30/2023]
Abstract
Cytokinins (CKs) are phytohormones that promote cell division and differentiation. However, the regulation of CK distribution and homeostasis in Brassica napus is poorly understood. Here, the endogenous CKs were first quantified by LC-ESI-MS/MS in rapeseed tissues and visualized by TCSn::GUS reporter lines. Interestingly, the cytokinin oxidase/dehydrogenase BnaCKX2 homologs were mainly expressed in reproductive organs. Subsequently, the quadruple mutants of the four BnaCKX2 homologs were generated. Endogenous CKs were increased in the seeds of the BnaCKX2 quadruple mutants, resulting in a significantly reduced seed size. In contrast, overexpression of BnaA9.CKX2 resulted in larger seeds, probably by delaying endosperm cellularization. Furthermore, the transcription factor BnaC6.WRKY10b, but not BnaC6.WRKY10a, positively regulated BnaA9.CKX2 expression by binding directly to its promoter region. Overexpression of BnaC6.WRKY10b rather than BnaC6.WRKY10a resulted in lower concentration of CKs and larger seeds by activating BnaA9.CKX2 expression, indicating that the functional differentiation of BnaWRKY10 homologs might have occurred during B. napus evolution or domestication. Notably, the haploid types of BnaA9.CKX2 were associated with 1000-seed weight in the natural B. napus population. Overall, the study reveals the distribution of CKs in B. napus tissues, and shows that BnaWRKY10-mediated BnaCKX2 expression is essential for seed size regulation, providing promising targets for oil crop improvement.
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Affiliation(s)
- Guanbo Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Sijia Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengya Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xia Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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25
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Peng L, Li X, Gao Y, Xie W, Zhang L, Song J, Li S, Zhao Z. Genome-Wide Identification of the RR Gene Family and Its Expression Analysis in Response to TDZ Induction in Rhododendron delavayi. PLANTS (BASEL, SWITZERLAND) 2023; 12:3250. [PMID: 37765414 PMCID: PMC10535058 DOI: 10.3390/plants12183250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023]
Abstract
The cytokinin response regulator (RR) gene is essential for cytokinin signal transduction, which plays a crucial role in plant growth and development. Here, we applied bioinformatics to Rhododendron delavayi's genome to identify its RR gene family and systematically analyzed their gene characteristics, phylogenetic evolution, chromosomal localization, collinearity analysis, promoter cis-elements, and expression patterns. Overall, 33 RdRR genes were distinguished and classified into three types. All these genes harbored motif 5 (YEVTTVNSGLEALELLRENKB), the most conserved one, along with the plant-conserved domain (REC domain), and could be mapped to 10 chromosomes with four gene pairs of segmental replication events but no tandem replication events; 13 RdRR genes showed collinearity with Arabidopsis thaliana genes. Promoter analysis revealed multiple hormone-related cis-elements in the RR genes. After a TDZ (thidiazuron) treatment, 13 genes had higher expression levels than the control, whose magnitude of change depended on the developmental stage of leaves' adventitious buds. The expression levels of RdRR14, RdRR17, RdRR20, and RdRR24 agreed with the average number of adventitious buds post-TDZ treatment. We speculate that these four genes could figure prominently in bud regeneration from R. delavayi leaves in vitro. This study provides detailed knowledge of RdRRs for research on cytokinin signaling and RdRR functioning in R. delavayi.
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Affiliation(s)
- Lvchun Peng
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming 650201, China;
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 650205, China
| | - Xuejiao Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Yan Gao
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China;
| | - Weijia Xie
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 650205, China
| | - Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 650205, China
| | - Jie Song
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 650205, China
| | - Shifeng Li
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming 650205, China
| | - Zhengxiong Zhao
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming 650201, China;
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China;
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26
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Rieger J, Fitz M, Fischer SM, Wallmeroth N, Flores-Romero H, Fischer NM, Brand LH, García-Sáez AJ, Berendzen KW, Mira-Rodado V. Exploring the Binding Affinity of the ARR2 GARP DNA Binding Domain via Comparative Methods. Genes (Basel) 2023; 14:1638. [PMID: 37628689 PMCID: PMC10454580 DOI: 10.3390/genes14081638] [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: 07/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure and function of this type of DNA-binding domain; thus, how ARRs bind to DNA at a structural level is still poorly understood. In order to understand how the MSP functions in planta, it is crucial to unravel both the kinetics as well as the structural identity of the components involved in such interactions. For this reason, this work focusses on resolving how the GARP domain of ARR2 (GARP2) binds to the promoter region of ARR5, one of its native target genes in cytokinin signaling. We have established that GARP2 specifically binds to the ARR5 promoter with three different bi-molecular interaction systems-qDPI-ELISA, FCS, and MST-and we also determined the KD of this interaction. In addition, structural modeling of the GARP2 domain confirms that GARP2 entails a HTH motif, and that protein-DNA interaction most likely occurs via the α3-helix and the N-terminal arm of this domain since mutations in this region hinder ARR2's ability to activate transcription.
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Affiliation(s)
- Janine Rieger
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Michael Fitz
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Stefan Markus Fischer
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Niklas Wallmeroth
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Hector Flores-Romero
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | - Nina Monika Fischer
- Institute for Bioinformatics and Medical Informatics, Tübingen University, 72076 Tübingen, Germany
| | - Luise Helene Brand
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Ana J. García-Sáez
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | | | - Virtudes Mira-Rodado
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
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27
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Dai Y, Luo L, Zhao Z. Genetic robustness control of auxin output in priming organ initiation. Proc Natl Acad Sci U S A 2023; 120:e2221606120. [PMID: 37399382 PMCID: PMC10334806 DOI: 10.1073/pnas.2221606120] [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: 12/20/2022] [Accepted: 05/17/2023] [Indexed: 07/05/2023] Open
Abstract
Auxin signaling is essential for organ initiation in plants. How genetic robustness controls auxin output during organ initiation is largely unknown. Here, we identified DORNROSCHEN-LIKE (DRNL) as a target of MONOPTEROS (MP) that plays essential roles in organ initiation. We demonstrate that MP physically interacts with DRNL to inhibit cytokinin accumulation by directly activating ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 and CYTOKININ OXIDASE 6. DRN, the paralogous gene of DRNL, acts redundantly with DRNL but is not coexpressed with DRNL in the organ founder cells in which DRNL is expressed. We demonstrate that DRNL directly inhibits DRN expression in the peripheral zone, whereas DRN transcripts are ectopically activated in drnl mutants and fully restore the functional deficiency of drnl in organ initiation. Our results provide a mechanistic framework for the robust control of auxin signaling in organ initiation through paralogous gene-triggered spatial gene compensation effects.
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Affiliation(s)
- Yuqiu Dai
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Ministry of Education Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, China
| | - Linjie Luo
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu241000, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu241000, China
| | - Zhong Zhao
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Ministry of Education Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, China
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28
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Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. SCIENCE ADVANCES 2023; 9:eadg6983. [PMID: 37418524 PMCID: PMC10328406 DOI: 10.1126/sciadv.adg6983] [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: 01/20/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2-based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency.
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Affiliation(s)
- Nao Ogura
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
| | - Yohei Sasagawa
- Department of Functional Genome Informatics, Division of Medical Genomics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
| | - Tasuku Ito
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Toshiaki Tameshige
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Yokohama 244-0813, Japan
| | - Satomi Kawai
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
| | - Masaki Sano
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
| | - Yuki Doll
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Biosciences and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Itoshi Nikaido
- Department of Functional Genome Informatics, Division of Medical Genomics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 119-0033, Japan
| | - Momoko Ikeuchi
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Biology, Faculty of Science, Niigata University, Niigata, Niigata 950-2181, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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29
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. BIODESIGN RESEARCH 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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30
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Tessi TM, Maurino VG, Shahriari M, Meissner E, Novak O, Pasternak T, Schumacher BS, Ditengou F, Li Z, Duerr J, Flubacher NS, Nautscher M, Williams A, Kazimierczak Z, Strnad M, Thumfart JO, Palme K, Desimone M, Teale WD. AZG1 is a cytokinin transporter that interacts with auxin transporter PIN1 and regulates the root stress response. THE NEW PHYTOLOGIST 2023; 238:1924-1941. [PMID: 36918499 DOI: 10.1111/nph.18879] [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: 10/27/2022] [Accepted: 01/29/2023] [Indexed: 05/04/2023]
Abstract
An environmentally responsive root system is crucial for plant growth and crop yield, especially in suboptimal soil conditions. This responsiveness enables the plant to exploit regions of high nutrient density while simultaneously minimizing abiotic stress. Despite the vital importance of root systems in regulating plant growth, significant gaps of knowledge exist in the mechanisms that regulate their architecture. Auxin defines both the frequency of lateral root (LR) initiation and the rate of LR outgrowth. Here, we describe a search for proteins that regulate root system architecture (RSA) by interacting directly with a key auxin transporter, PIN1. The native separation of Arabidopsis plasma membrane protein complexes identified several PIN1 co-purifying proteins. Among them, AZG1 was subsequently confirmed as a PIN1 interactor. Here, we show that, in Arabidopsis, AZG1 is a cytokinin (CK) import protein that co-localizes with and stabilizes PIN1, linking auxin and CK transport streams. AZG1 expression in LR primordia is sensitive to NaCl, and the frequency of LRs is AZG1-dependent under salt stress. This report therefore identifies a potential point for auxin:cytokinin crosstalk, which shapes RSA in response to NaCl.
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Affiliation(s)
- Tomás M Tessi
- Instituto Multidisciplinario de Biología Vegetal, Velez Sarsfield 249, 5000, Córdoba, Argentina
| | - Veronica G Maurino
- Molecular Plant Physiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Mojgan Shahriari
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Esther Meissner
- Conservation Ecology, Department Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35032, Marburg, Germany
| | - Ondrej Novak
- Laboratory of Growth Regulators, Institute of Experimental Botany ASCR and Palacky, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Taras Pasternak
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Benjamin S Schumacher
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Franck Ditengou
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Zenglin Li
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Jasmin Duerr
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Noemi S Flubacher
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Moritz Nautscher
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Alyssa Williams
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Zuzanna Kazimierczak
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany ASCR and Palacky, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Jörg-Oliver Thumfart
- Faculty of Medicine, Institute of Physiology II, University of Freiburg, Hermann-Herder-Strasse 7, 79104, Freiburg, Germany
- Labormedizinisches Zentrum Ostschweiz, Lagerstrasse 30, 9470, Buchs, SG, Switzerland
| | - Klaus Palme
- Molecular Plant Physiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Centre of Biological Systems Analysis, University of Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Marcelo Desimone
- Instituto Multidisciplinario de Biología Vegetal, Velez Sarsfield 249, 5000, Córdoba, Argentina
| | - William D Teale
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
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31
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Abstract
Proteins are workhorses in the cell; they form stable and more often dynamic, transient protein-protein interactions, assemblies, and networks and have an intimate interplay with DNA and RNA. These network interactions underlie fundamental biological processes and play essential roles in cellular function. The proximity-dependent biotinylation labeling approach combined with mass spectrometry (PL-MS) has recently emerged as a powerful technique to dissect the complex cellular network at the molecular level. In PL-MS, by fusing a genetically encoded proximity-labeling (PL) enzyme to a protein or a localization signal peptide, the enzyme is targeted to a protein complex of interest or to an organelle, allowing labeling of proximity proteins within a zoom radius. These biotinylated proteins can then be captured by streptavidin beads and identified and quantified by mass spectrometry. Recently engineered PL enzymes such as TurboID have a much-improved enzymatic activity, enabling spatiotemporal mapping with a dramatically increased signal-to-noise ratio. PL-MS has revolutionized the way we perform proteomics by overcoming several hurdles imposed by traditional technology, such as biochemical fractionation and affinity purification mass spectrometry. In this review, we focus on biotin ligase-based PL-MS applications that have been, or are likely to be, adopted by the plant field. We discuss the experimental designs and review the different choices for engineered biotin ligases, enrichment, and quantification strategies. Lastly, we review the validation and discuss future perspectives.
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Affiliation(s)
- Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Sumudu S Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Pei-Qiao Xie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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32
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Ohashi-Ito K, Iwamoto K, Yamagami A, Nakano T, Fukuda H. HD-ZIP III-dependent local promotion of brassinosteroid synthesis suppresses vascular cell division in Arabidopsis root apical meristem. Proc Natl Acad Sci U S A 2023; 120:e2216632120. [PMID: 37011193 PMCID: PMC10104508 DOI: 10.1073/pnas.2216632120] [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: 09/29/2022] [Accepted: 02/22/2023] [Indexed: 04/05/2023] Open
Abstract
Spatiotemporal control of cell division in the meristem is vital for plant growth. In the stele of the root apical meristem (RAM), procambial cells divide periclinally to increase the number of vascular cell files. Class III homeodomain leucine zipper (HD-ZIP III) proteins are key transcriptional regulators of RAM development and suppress the periclinal division of vascular cells in the stele; however, the mechanism underlying the regulation of vascular cell division by HD-ZIP III transcription factors (TFs) remains largely unknown. Here, we performed transcriptome analysis to identify downstream genes of HD-ZIP III and found that HD-ZIP III TFs positively regulate brassinosteroid biosynthesis-related genes, such as CONSTITUTIVE PHOTOMORPHOGENIC DWARF (CPD), in vascular cells. Introduction of pREVOLUTA::CPD in a quadruple loss-of-function mutant of HD-ZIP III genes partly rescued the phenotype in terms of the vascular defect in the RAM. Treatment of a quadruple loss-of-function mutant, a gain-of-function mutant of HD-ZIP III, and the wild type with brassinosteroid and a brassinosteroid synthesis inhibitor also indicated that HD-ZIP III TFs act together to suppress vascular cell division by increasing brassinosteroid levels. Furthermore, brassinosteroid application suppressed the cytokinin response in vascular cells. Together, our findings suggest that the suppression of vascular cell division by HD-ZIP III TFs is caused, at least in part, by the increase in brassinosteroid levels through the transcriptional activation of brassinosteroid biosynthesis genes in the vascular cells of the RAM. This elevated brassinosteroid level suppresses cytokinin response in vascular cells, inhibiting vascular cell division in the RAM.
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Affiliation(s)
- Kyoko Ohashi-Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Kuninori Iwamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Ayumi Yamagami
- Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Kyoto606-8502, Japan
| | - Takeshi Nakano
- Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Kyoto606-8502, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
- Department of Bioscience and Biotechnology, Faculty of Environmental Sciences, Kyoto University of Advanced Science, Kyoto621-8555, Japan
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33
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Fujiwara M, Imamura M, Matsushita K, Roszak P, Yamashino T, Hosokawa Y, Nakajima K, Fujimoto K, Miyashima S. Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis. Curr Biol 2023; 33:886-898.e8. [PMID: 36787744 DOI: 10.1016/j.cub.2023.01.036] [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: 08/25/2022] [Revised: 11/24/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023]
Abstract
Symmetric tissue alignment is pivotal to the functions of plant vascular tissue, such as long-distance molecular transport and lateral organ formation. During the vascular development of the Arabidopsis roots, cytokinins initially determine cell-type boundaries among vascular stem cells and subsequently promote cell proliferation to establish vascular tissue symmetry. Although it is unknown whether and how the symmetry of initially defined boundaries is progressively refined under tissue growth in plants, such boundary shapes in animal tissues are regulated by cell fluidity, e.g., cell migration and intercalation, lacking in plant tissues. Here, we uncover that cell proliferation during vascular development produces anisotropic compressive stress, smoothing, and symmetrizing cell arrangement of the vascular-cell-type boundary. Mechanistically, the GATA transcription factor HANABA-TARANU cooperates with the type-B Arabidopsis response regulators to form an incoherent feedforward loop in cytokinin signaling. The incoherent feedforward loop fine-tunes the position and frequency of vascular cell proliferation, which in turn restricts the source of mechanical stress to the position distal and symmetric to the boundary. By combinatorial analyses of mechanical simulations and laser cell ablation, we show that the spatially constrained environment of vascular tissue efficiently entrains the stress orientation among the cells to produce a tissue-wide stress field. Together, our data indicate that the localized proliferation regulated by the cytokinin signaling circuit is decoded into a globally oriented mechanical stress to shape the vascular tissue symmetry, representing a reasonable mechanism controlling the boundary alignment and symmetry in tissue lacking cell fluidity.
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Affiliation(s)
- Motohiro Fujiwara
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Miyu Imamura
- Laboratory of Molecular and Functional Genomics, Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Katsuyoshi Matsushita
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Pawel Roszak
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, United Kingdom; Faculty of Biological and Environmental Sciences, University of Helsinki 00014, Helsinki, Finland
| | - Takafumi Yamashino
- Laboratory of Molecular and Functional Genomics, Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yoichiroh Hosokawa
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Koichi Fujimoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka 560-0043, Japan.
| | - Shunsuke Miyashima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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34
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Hirano T, Okamoto A, Oda Y, Sakamoto T, Takeda S, Matsuura T, Ikeda Y, Higaki T, Kimura S, Sato MH. Ab-GALFA, A bioassay for insect gall formation using the model plant Arabidopsis thaliana. Sci Rep 2023; 13:2554. [PMID: 36781988 PMCID: PMC9925437 DOI: 10.1038/s41598-023-29302-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
Insect galls are abnormal plant organs formed by gall-inducing insects to provide shelter and nutrients for themselves. Although insect galls are spatialized complex structures with unique shapes and functions, the molecular mechanism of the gall formation and the screening system for the gall inducing effectors remains unknown. Here, we demonstrate that an extract of a gall-inducing aphid, Schlechtendalia chinensis, induces an abnormal structure in the root-tip region of Arabidopsis seedlings. The abnormal structure is composed of stem-like cells, vascular, and protective tissues, as observed in typical insect galls. Furthermore, we confirm similarities in the gene expression profiles between the aphid-treated seedlings and the early developmental stages of Rhus javanica galls formed by S. chinensis. Based on the results, we propose a model system for analyzing the molecular mechanisms of gall formation: the Arabidopsis-based Gall-Forming Assay (Ab-GALFA). Ab-GALFA could be used not only as a model to elucidate the mechanisms underlying gall formation, but also as a bioassay system to isolate insect effector molecules of gall-induction.
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Affiliation(s)
- Tomoko Hirano
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-Hangi-Cho, Sakyo-Ku, Kyoto, 606-8522, Japan
- Center for Frontier Natural History, Kyoto Prefectural University, Shimogamo-Hangi-Cho, Sakyo-Ku, Kyoto, 606-8522, Japan
| | - Ayaka Okamoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-Hangi-Cho, Sakyo-Ku, Kyoto, 606-8522, Japan
| | - Yoshihisa Oda
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Tomoaki Sakamoto
- Laboratory of Plant Ecological and Evolutionary Developmental Biology, Department of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, 603-8555, Japan
| | - Seiji Takeda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-Hangi-Cho, Sakyo-Ku, Kyoto, 606-8522, Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 74 Oji, Kitainayazuma, Seika-Cho, Soraku-Gun, Kyoto, 619-0244, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
| | - Takumi Higaki
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Seisuke Kimura
- Laboratory of Plant Ecological and Evolutionary Developmental Biology, Department of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, 603-8555, Japan
| | - Masa H Sato
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo-Hangi-Cho, Sakyo-Ku, Kyoto, 606-8522, Japan.
- Center for Frontier Natural History, Kyoto Prefectural University, Shimogamo-Hangi-Cho, Sakyo-Ku, Kyoto, 606-8522, Japan.
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35
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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36
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Navarro-Cartagena S, Micol JL. Is auxin enough? Cytokinins and margin patterning in simple leaves. TRENDS IN PLANT SCIENCE 2023; 28:54-73. [PMID: 36180378 DOI: 10.1016/j.tplants.2022.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
The interplay between auxin and cytokinins affects facets of plant development as different as ovule formation and lateral root initiation. Moreover, cytokinins favor complexity in the development of Solanum lycopersicum and Cardamine hirsuta compound leaves. Nevertheless, no role has been proposed for cytokinins in patterning the margins of the simple leaves of Arabidopsis thaliana, a process that is assumed to be sufficiently explained by auxin localization. Here, we discuss evidence supporting the hypothesis that cytokinins play a role in simple leaf margin morphogenesis via crosstalk with auxin, as occurs in other plant developmental events. Indeed, mutant or transgenic arabidopsis plants defective in cytokinin biosynthesis or signaling, or with increased cytokinin degradation have leaf margins less serrated than the wild type.
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Affiliation(s)
- Sergio Navarro-Cartagena
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain.
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37
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Zhang K, Zhang H, Pan Y, Niu Y, Guo L, Ma Y, Tian S, Wei J, Wang C, Yang X, Fu Y, Qu P, Liu L, Zhang Y, Sun H, Bai Z, Dong J, Li C, Liu X. Cell- and noncell-autonomous AUXIN RESPONSE FACTOR3 controls meristem proliferation and phyllotactic patterns. PLANT PHYSIOLOGY 2022; 190:2335-2349. [PMID: 35972411 PMCID: PMC9706454 DOI: 10.1093/plphys/kiac370] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In cell-cell communication, noncell-autonomous transcription factors play vital roles in controlling plant stem cell fate. We previously reported that AUXIN RESPONSE FACTOR3 (ARF3), a member of the ARF family with critical roles in floral meristem maintenance and determinacy, has a distinct accumulation pattern that differs from the expression domain of its encoding gene in the shoot apical meristem (SAM). However, the biological meaning of this difference is obscure. Here, we demonstrate that ARF3 expression in Arabidopsis (Arabidopsis thaliana) is mainly activated at the periphery of the SAM by auxin where ARF3 cell autonomously regulates the expression of meristem-organ boundary-specific genes, such as CUP-SHAPED COTYLEDON1-3 (CUC1-3), BLADE ON PETIOLE1-2 (BOP1-2), and TARGETS UNDER ETTIN CONTROL3 (TEC3) to regulate the arrangement of organs in regular pattern, a phenomenon referred to as phyllotaxis. We also show that ARF3 is translocated into the organizing center where it represses cytokinin activity and WUSCHEL expression to regulate meristem activity noncell-autonomously. Therefore, ARF3 acts as a molecular link that mediates the interaction of auxin and cytokinin signaling in the SAM while coordinating the balance between meristem maintenance and organogenesis. Our findings reveal an ARF3-mediated coordination mechanism through cell-cell communication in dynamic SAM maintenance.
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Affiliation(s)
- Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Hao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yanyun Pan
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yuru Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Shijun Tian
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Jiarong Wei
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Cong Wang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Xiubo Yang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Yunze Fu
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Ping Qu
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Liantao Liu
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Yongjiang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Hongchun Sun
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Zhiying Bai
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Cundong Li
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
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38
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Dow L, Barrow RA, White RG, Mathesius U. Photolysis of caged cytokinin in single cells of Arabidopsis thaliana. PLANT METHODS 2022; 18:120. [PMID: 36369052 PMCID: PMC9652950 DOI: 10.1186/s13007-022-00953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Cytokinins are a class of phytohormone that play a crucial role in the development of plants. They are involved in the regulation of nearly every aspect of plant growth, from germination to senescence. The role of cytokinins in many developmental programs is complex and varies both spatially and temporally. Current techniques used to investigate the functions of cytokinins in plant development lack this spatial and temporal resolution required to observe cell-type specific effects. RESULTS To this end, we present a method of activating a caged cytokinin in single cells. A caged benzyladenine was synthesized, along with caged adenine as a negative control. In vitro testing confirmed ultraviolet light-mediated uncaging, and subsequent root growth assays demonstrated that uncaging produced a cytokinin phenotype. This uncaging was confined to single cells using multiphoton confocal microscopy. Using an Arabidopsis thaliana cytokinin reporter line expressing TCSn::GFP, the resulting GFP expression was confined to the uncaging region, including in single cells. This study presents a novel cell-targeted method of cytokinin delivery, which has the potential to elucidate a broad range of processes in plant development. CONCLUSIONS We combined multiphoton confocal microscopy and a caged cytokinin treatment, allowing cell type-specific uncaging of a cytokinin in Arabidopsis roots.
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Affiliation(s)
- Lachlan Dow
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Russell A Barrow
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Rosemary G White
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
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39
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Liu Y, Yuan G, Hassan MM, Abraham PE, Mitchell JC, Jacobson D, Tuskan GA, Khakhar A, Medford J, Zhao C, Liu CJ, Eckert CA, Doktycz MJ, Tschaplinski TJ, Yang X. Biological and Molecular Components for Genetically Engineering Biosensors in Plants. BIODESIGN RESEARCH 2022; 2022:9863496. [PMID: 37850147 PMCID: PMC10521658 DOI: 10.34133/2022/9863496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/08/2022] [Indexed: 10/19/2023] Open
Abstract
Plants adapt to their changing environments by sensing and responding to physical, biological, and chemical stimuli. Due to their sessile lifestyles, plants experience a vast array of external stimuli and selectively perceive and respond to specific signals. By repurposing the logic circuitry and biological and molecular components used by plants in nature, genetically encoded plant-based biosensors (GEPBs) have been developed by directing signal recognition mechanisms into carefully assembled outcomes that are easily detected. GEPBs allow for in vivo monitoring of biological processes in plants to facilitate basic studies of plant growth and development. GEPBs are also useful for environmental monitoring, plant abiotic and biotic stress management, and accelerating design-build-test-learn cycles of plant bioengineering. With the advent of synthetic biology, biological and molecular components derived from alternate natural organisms (e.g., microbes) and/or de novo parts have been used to build GEPBs. In this review, we summarize the framework for engineering different types of GEPBs. We then highlight representative validated biological components for building plant-based biosensors, along with various applications of plant-based biosensors in basic and applied plant science research. Finally, we discuss challenges and strategies for the identification and design of biological components for plant-based biosensors.
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Affiliation(s)
- Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - June Medford
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Cheng Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Carrie A. Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Romanov GA. Perception, Transduction and Crosstalk of Auxin and Cytokinin Signals. Int J Mol Sci 2022; 23:13150. [PMID: 36361937 PMCID: PMC9656646 DOI: 10.3390/ijms232113150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 09/01/2024] Open
Abstract
Auxins and cytokinins are considered the most important plant hormones, responsible for fundamental traits of the plant organism [...].
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Affiliation(s)
- Georgy A Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
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41
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Antoniadi I, Mateo-Bonmatí E, Pernisová M, Brunoni F, Antoniadi M, Villalonga MGA, Ament A, Karády M, Turnbull C, Doležal K, Pěnčík A, Ljung K, Novák O. IPT9, a cis-zeatin cytokinin biosynthesis gene, promotes root growth. FRONTIERS IN PLANT SCIENCE 2022; 13:932008. [PMID: 36311087 PMCID: PMC9616112 DOI: 10.3389/fpls.2022.932008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/16/2022] [Indexed: 06/12/2023]
Abstract
Cytokinin and auxin are plant hormones that coordinate many aspects of plant development. Their interactions in plant underground growth are well established, occurring at the levels of metabolism, signaling, and transport. Unlike many plant hormone classes, cytokinins are represented by more than one active molecule. Multiple mutant lines, blocking specific parts of cytokinin biosynthetic pathways, have enabled research in plants with deficiencies in specific cytokinin-types. While most of these mutants have confirmed the impeding effect of cytokinin on root growth, the ipt29 double mutant instead surprisingly exhibits reduced primary root length compared to the wild type. This mutant is impaired in cis-zeatin (cZ) production, a cytokinin-type that had been considered inactive in the past. Here we have further investigated the intriguing ipt29 root phenotype, opposite to known cytokinin functions, and the (bio)activity of cZ. Our data suggest that despite the ipt29 short-root phenotype, cZ application has a negative impact on primary root growth and can activate a cytokinin response in the stele. Grafting experiments revealed that the root phenotype of ipt29 depends mainly on local signaling which does not relate directly to cytokinin levels. Notably, ipt29 displayed increased auxin levels in the root tissue. Moreover, analyses of the differential contributions of ipt2 and ipt9 to the ipt29 short-root phenotype demonstrated that, despite its deficiency on cZ levels, ipt2 does not show any root phenotype or auxin homeostasis variation, while ipt9 mutants were indistinguishable from ipt29. We conclude that IPT9 functions may go beyond cZ biosynthesis, directly or indirectly, implicating effects on auxin homeostasis and therefore influencing plant growth.
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Affiliation(s)
- Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Eduardo Mateo-Bonmatí
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Markéta Pernisová
- Plant Sciences Core Facility, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), and NCBR, Faculty of Science, Masaryk University, Brno, Czechia
| | - Federica Brunoni
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Mariana Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Anita Ament
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Michal Karády
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Colin Turnbull
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Karel Doležal
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
- Department of Chemical Biology, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Olomouc, Czechia
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42
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Controlling gene expression with deep generative design of regulatory DNA. Nat Commun 2022; 13:5099. [PMID: 36042233 PMCID: PMC9427793 DOI: 10.1038/s41467-022-32818-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Using mutagenesis typically requires screening sizable random DNA libraries, which limits the designs to span merely a short section of the promoter and restricts their control of gene expression. Here, we prototype a deep learning strategy based on generative adversarial networks (GAN) by learning directly from genomic and transcriptomic data. Our ExpressionGAN can traverse the entire regulatory sequence-expression landscape in a gene-specific manner, generating regulatory DNA with prespecified target mRNA levels spanning the whole gene regulatory structure including coding and adjacent non-coding regions. Despite high sequence divergence from natural DNA, in vivo measurements show that 57% of the highly-expressed synthetic sequences surpass the expression levels of highly-expressed natural controls. This demonstrates the applicability and relevance of deep generative design to expand our knowledge and control of gene expression regulation in any desired organism, condition or tissue. Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Here the authors present EspressionGAN, a generative adversarial network that uses genomic and transcriptomic data to generate regulatory sequences.
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Jardinaud MF, Fromentin J, Auriac MC, Moreau S, Pecrix Y, Taconnat L, Cottret L, Aubert G, Balzergue S, Burstin J, Carrere S, Gamas P. MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development. PLANT PHYSIOLOGY 2022; 189:1587-1607. [PMID: 35471237 PMCID: PMC9237690 DOI: 10.1093/plphys/kiac177] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2022] [Indexed: 05/31/2023]
Abstract
Rhizobium-legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.
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Affiliation(s)
| | | | | | - Sandra Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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44
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Bellande K, Trinh DC, Gonzalez AA, Dubois E, Petitot AS, Lucas M, Champion A, Gantet P, Laplaze L, Guyomarc’h S. PUCHI represses early meristem formation in developing lateral roots of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3496-3510. [PMID: 35224628 PMCID: PMC9162184 DOI: 10.1093/jxb/erac079] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/25/2022] [Indexed: 05/21/2023]
Abstract
Lateral root organogenesis is a key process in the development of a plant's root system and its adaptation to the environment. During lateral root formation, an early phase of cell proliferation first produces a four-cell-layered primordium, and only from this stage onwards is a root meristem-like structure, expressing root stem cell niche marker genes, being established in the developing organ. Previous studies reported that the gene regulatory network controlling lateral root formation is organized into two subnetworks whose mutual inhibition may contribute to organ patterning. PUCHI encodes an AP2/ERF transcription factor expressed early during lateral root primordium development and required for correct lateral root formation. To dissect the molecular events occurring during this early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 mutants and wild types. Transcriptomic and reporter analyses revealed that meristem-related genes were expressed ectopically at early stages of lateral root formation in puchi-1 mutants. We conclude that, consistent with the inhibition of genetic modules contributing to lateral root development, PUCHI represses ectopic establishment of meristematic cell identities at early stages of organ development. These findings shed light on gene network properties that orchestrate correct timing and patterning during lateral root formation.
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Affiliation(s)
| | | | - Anne-Alicia Gonzalez
- Univ Montpellier, CNRS, INSERM, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | - Emeric Dubois
- Univ Montpellier, CNRS, INSERM, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | - Mikaël Lucas
- DIADE, Univ Montpellier, IRD, Montpellier, France
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Banwarth-Kuhn M, Rodriguez K, Michael C, Ta CK, Plong A, Bourgain-Chang E, Nematbakhsh A, Chen W, Roy-Chowdhury A, Reddy GV, Alber M. Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance. PLoS Comput Biol 2022; 18:e1010199. [PMID: 35727850 PMCID: PMC9249181 DOI: 10.1371/journal.pcbi.1010199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 07/01/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Stem cell maintenance in multilayered shoot apical meristems (SAMs) of plants requires strict regulation of cell growth and division. Exactly how the complex milieu of chemical and mechanical signals interact in the central region of the SAM to regulate cell division plane orientation is not well understood. In this paper, simulations using a newly developed multiscale computational model are combined with experimental studies to suggest and test three hypothesized mechanisms for the regulation of cell division plane orientation and the direction of anisotropic cell expansion in the corpus. Simulations predict that in the Apical corpus, WUSCHEL and cytokinin regulate the direction of anisotropic cell expansion, and cells divide according to tensile stress on the cell wall. In the Basal corpus, model simulations suggest dual roles for WUSCHEL and cytokinin in regulating both the direction of anisotropic cell expansion and cell division plane orientation. Simulation results are followed by a detailed analysis of changes in cell characteristics upon manipulation of WUSCHEL and cytokinin in experiments that support model predictions. Moreover, simulations predict that this layer-specific mechanism maintains both the experimentally observed shape and structure of the SAM as well as the distribution of WUSCHEL in the tissue. This provides an additional link between the roles of WUSCHEL, cytokinin, and mechanical stress in regulating SAM growth and proper stem cell maintenance in the SAM.
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Affiliation(s)
- Mikahl Banwarth-Kuhn
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Applied Mathematics, University of California, Merced, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Kevin Rodriguez
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Christian Michael
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Calvin-Khang Ta
- Computer Science and Engineering Department, University of California, Riverside, California, United States of America
| | - Alexander Plong
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Eric Bourgain-Chang
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Ali Nematbakhsh
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Weitao Chen
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
| | - Amit Roy-Chowdhury
- Computer Science and Engineering Department, University of California, Riverside, California, United States of America
- Department of Electrical and Computer Engineering, University of California, Riverside, California, United States of America
| | - G. Venugopala Reddy
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Mark Alber
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, California, United States of America
- Department of Mathematics, University of California, Riverside, California, United States of America
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46
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ADA2b and GCN5 Affect Cytokinin Signaling by Modulating Histone Acetylation and Gene Expression during Root Growth of Arabidopsis thaliana. PLANTS 2022; 11:plants11101335. [PMID: 35631760 PMCID: PMC9148027 DOI: 10.3390/plants11101335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022]
Abstract
In Arabidopsis thaliana, the histone acetyltransferase GCN5 and the associated coactivator ADA2b regulate root growth and affect gene expression. The cytokinin signaling reporter TCS::GFP was introduced into gcn5-1, ada2b-1, and ada2a-2, as well as the ada2a-2ada2b-1 mutants. The early root growth (4 to 7 days post-germination) was analyzed using cellular and molecular approaches. TCS signal accumulated from the fourth to seventh days of root growth in the wild-type columella cells. In contrast, ada2b-1 and gcn5-1 and ada2a-2ada2b-1 double mutants displayed reduced TCS expression relative to wild type. Gene expression analysis showed that genes associated with cytokinin homeostasis were downregulated in the roots of gcn5-1 and ada2b-1 mutants compared to wild-type plants. H3K14 acetylation was affected in the promoters of cytokinin synthesis and catabolism genes during root growth of Arabidopsis. Therefore, GCN5 and ADA2b are positive regulators of cytokinin signaling during root growth by modulating histone acetylation and the expression of genes involved in cytokinin synthesis and catabolism. Auxin application in the roots of wild-type seedlings increased TCS::GFP expression. In contrast, ada2b and ada2ada2b mutant plants do not show the auxin-induced TCS signal, suggesting that GCN5 and ADA2b are required for the auxin-induced cytokinin signaling in early root growth.
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47
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Kořínková N, Fontana IM, Nguyen TD, Pouramini P, Bergougnoux V, Hensel G. Enhancing cereal productivity by genetic modification of root architecture. Biotechnol J 2022; 17:e2100505. [PMID: 35537849 DOI: 10.1002/biot.202100505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/03/2022] [Accepted: 04/23/2022] [Indexed: 11/06/2022]
Abstract
Food security is one of the main topics of today's agriculture, primarily due to increasingly challenging environmental conditions. As most of humankind has a daily intake of cereal grains, current breeding programs focus on these crop plants. Customised endonucleases have been included in the breeders' toolbox after successfully demonstrating their use. Due to technological restrictions, the main focus of the new technology was on above-ground plant organs. In contrast, the essential below ground components were given only limited attention. In the present review, the knowledge of the root system architecture in cereals and the role of phytohormones during their establishment is summarized, and the underlying molecular mechanisms are outlined. The review summarizes how the use of CRISPR-based genome editing methodology can improve the root system architecture to enhance crop production genetically. Finally, future research directions involving this knowledge and technical advances are suggested. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nikola Kořínková
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371
| | - Irene M Fontana
- Leibniz Institute of Plant Genetics and Crop Plant Research, Plant Reproductive Biology, D-06466 Seeland OT, Gatersleben
| | - Thu D Nguyen
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371
| | - Pouneh Pouramini
- Leibniz Institute of Plant Genetics and Crop Plant Research, Plant Reproductive Biology, D-06466 Seeland OT, Gatersleben
| | - Véronique Bergougnoux
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371
| | - Goetz Hensel
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, D-40225, Dusseldorf
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48
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Dai X, Wang J, Wang L, Liu Z, Li Q, Cai Y, Li S, Xiang F. HY5 inhibits in vitro shoot stem cell niches initiation via directly repressing pluripotency and cytokinin pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:781-801. [PMID: 35132706 DOI: 10.1111/tpj.15703] [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: 05/16/2021] [Revised: 01/22/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The efficiency of plant regeneration from explants is influenced by phytohormones and environmental conditions. Light has a particularly marked effect on in vitro shoot regeneration, and some light signaling factors are involved in shoot regeneration, while the underlying molecular mechanism remains elusive. Here, ELONGATED HYPOCOTYL5 (HY5), as the key transcription factor of light signaling, was found to inhibit shoot regeneration under a range of light conditions. The heightened shoot regeneration capacity of the hy5-215 mutant was less marked in the dark than in the light, showing that HY5-mediated inhibition of shoot regeneration is partly light dependent. The co-localization of WUSCHEL (WUS) and CLAVATA3 (CLV3) expressions was found to coincide with the initiation of stem cell niches in root explants during shoot regeneration. HY5 could directly repress CLV3 and WUS expression by binding to their respective promoters. In parallel, HY5 indirectly repressed CLV3 and WUS by binding to the ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) promoter. The resulting dual regulation exerted by HY5 on WUS and CLV3 impeded the initiation of shoot stem cell niches. A HY5-mediated inhibitory pathway was identified that links cytokinin signaling and the pluripotency pathway during shoot regeneration.
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Affiliation(s)
- Xuehuan Dai
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Jing Wang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
| | - Lili Wang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
| | - Zhenhua Liu
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, 250355, China
| | - Qiang Li
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
| | - Yunfei Cai
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
- School of Life Sciences, Qilu Normal University, Jinan, Shandong Province, 250000, China
| | - Shuo Li
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
| | - Fengning Xiang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong Province, 266237, China
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49
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Timilsina R, Kim Y, Park S, Park H, Park SJ, Kim JH, Park JH, Kim D, Park YI, Hwang D, Lee JC, Woo HR. ORESARA 15, a PLATZ transcription factor, controls root meristem size through auxin and cytokinin signalling-related pathways. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2511-2524. [PMID: 35139177 DOI: 10.1093/jxb/erac050] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
An optimal size of post-embryonic root apical meristem (RAM) is achieved by a balance between cell division and differentiation. Despite extensive research, molecular mechanisms underlying the coordination of cell division and differentiation are still fragmentary. Here, we report that ORESARA 15 (ORE15), an Arabidopsis PLANT A/T-RICH SEQUENCE-AND ZINC-BINDING PROTEIN (PLATZ) transcription factor preferentially expressed in the RAM, determines RAM size. Primary root length, RAM size, cell division rate, and stem cell niche activity were reduced in an ore15 loss-of-function mutant but enhanced in an activation-tagged line overexpressing ORE15, compared with wild type. ORE15 forms mutually positive and negative feedback loops with auxin and cytokinin signalling, respectively. Collectively, our findings imply that ORE15 controls RAM size by mediating the antagonistic interaction between auxin and cytokinin signalling-related pathways.
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Affiliation(s)
- Rupak Timilsina
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Yongmin Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Sanghoon Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Hyunsoo Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Sung-Jin Park
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Ji-Hwan Park
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Doa Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Chan Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
- New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
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50
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Rahimi A, Karami O, Lestari AD, de Werk T, Amakorová P, Shi D, Novák O, Greb T, Offringa R. Control of cambium initiation and activity in Arabidopsis by the transcriptional regulator AHL15. Curr Biol 2022; 32:1764-1775.e3. [PMID: 35294866 DOI: 10.1016/j.cub.2022.02.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/10/2021] [Accepted: 02/22/2022] [Indexed: 01/10/2023]
Abstract
Plant secondary growth, which is the basis of wood formation, includes the production of secondary xylem, which is derived from meristematic cambium cells embedded in vascular tissue. Here, we identified an important role for the Arabidopsis thaliana (Arabidopsis) AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) transcriptional regulator in controlling vascular cambium activity. The limited secondary xylem development in inflorescence stems of herbaceous Arabidopsis plants was significantly reduced in ahl15 loss-of-function mutants, whereas constitutive or vascular meristem-specific AHL15 overexpression produced woody inflorescence stems. AHL15 was required for enhanced secondary xylem formation in the woody suppressor of overexpression of constans 1 (soc1) fruitfull (ful) double loss-of-function mutant. Moreover, we found that AHL15 induces vascular cambium activity downstream of the repressing SOC1 and FUL transcription factors, most likely similar to how it enhances lateral branching by promoting biosynthesis of the hormone cytokinin. Our results uncover a novel pathway driving cambium development, in which AHL15 expression levels act in parallel to and are dependent on the well-established TDIF-PXY-WOX pathway to differentiate between herbaceous and woody stem growth.
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Affiliation(s)
- Arezoo Rahimi
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
| | - Angga Dwituti Lestari
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Tobias de Werk
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Petra Amakorová
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, 78371 Olomouc, Czech Republic
| | - Dongbo Shi
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, 78371 Olomouc, Czech Republic
| | - Thomas Greb
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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