1
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Hountalas JE, Lumba S. Mixing and matching SMXL proteins to fine-tune strigolactone responses. MOLECULAR PLANT 2024; 17:1167-1169. [PMID: 38898655 DOI: 10.1016/j.molp.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/04/2024] [Accepted: 06/17/2024] [Indexed: 06/21/2024]
Affiliation(s)
- Jenna E Hountalas
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Shelley Lumba
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
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2
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Hunziker P, Greb T. Stem Cells and Differentiation in Vascular Tissues. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:399-425. [PMID: 38382908 DOI: 10.1146/annurev-arplant-070523-040525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Plant vascular tissues are crucial for the long-distance transport of water, nutrients, and a multitude of signal molecules throughout the plant body and, therefore, central to plant growth and development. The intricate development of vascular tissues is orchestrated by unique populations of dedicated stem cells integrating endogenous as well as environmental cues. This review summarizes our current understanding of vascular-related stem cell biology and of vascular tissue differentiation. We present an overview of the molecular and cellular mechanisms governing the maintenance and fate determination of vascular stem cells and highlight the interplay between intrinsic and external cues. In this context, we emphasize the role of transcription factors, hormonal signaling, and epigenetic modifications. We also discuss emerging technologies and the large repertoire of cell types associated with vascular tissues, which have the potential to provide unprecedented insights into cellular specialization and anatomical adaptations to distinct ecological niches.
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Affiliation(s)
- Pascal Hunziker
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany; ,
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany; ,
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3
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Basso MF, Girardin G, Vergata C, Buti M, Martinelli F. Genome-wide transcript expression analysis reveals major chickpea and lentil genes associated with plant branching. FRONTIERS IN PLANT SCIENCE 2024; 15:1384237. [PMID: 38962245 PMCID: PMC11220206 DOI: 10.3389/fpls.2024.1384237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
The search for elite cultivars with better architecture has been a demand by farmers of the chickpea and lentil crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. Herein, this work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested. A total of 1,624 and 2,512 transcripts were identified as differentially expressed among different tissues and contrasting cultivars of chickpea and lentil, respectively. Several gene categories were significantly modulated such as cell cycle, DNA transcription, energy metabolism, hormonal biosynthesis and signaling, proteolysis, and vegetative development between apical and axillary tissues and contrasting cultivars of chickpea and lentil. Based on differential expression and branching-associated biological function, ten chickpea genes and seven lentil genes were considered the main players involved in differentially regulating the plant branching between contrasting cultivars. These collective data putatively revealed the general mechanism and high-effect genes associated with the regulation of branching in chickpea and lentil, which are potential targets for manipulation through genome editing and transgenesis aiming to improve plant architecture.
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Affiliation(s)
| | | | - Chiara Vergata
- Department of Biology, University of Florence, Florence, Italy
| | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
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4
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Han E, Geng Z, Qin Y, Wang Y, Ma S. Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism. PLANT COMMUNICATIONS 2024:100978. [PMID: 38783601 DOI: 10.1016/j.xplc.2024.100978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/24/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
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Affiliation(s)
- Ershang Han
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Zhenxing Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yue Qin
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yuewei Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Shisong Ma
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230027, China.
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5
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Guillory A, Lopez-Obando M, Bouchenine K, Le Bris P, Lécureuil A, Pillot JP, Steinmetz V, Boyer FD, Rameau C, de Saint Germain A, Bonhomme S. SUPPRESSOR OF MAX2 1-LIKE (SMXL) homologs are MAX2-dependent repressors of Physcomitrium patens growth. THE PLANT CELL 2024; 36:1655-1672. [PMID: 38242840 PMCID: PMC11062456 DOI: 10.1093/plcell/koae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024]
Abstract
SUPPRESSOR OF MAX2 (SMAX)1-LIKE (SMXL) proteins are a plant-specific clade of type I HSP100/Clp-ATPases. SMXL genes are present in virtually all land plant genomes. However, they have mainly been studied in angiosperms. In Arabidopsis (Arabidopsis thaliana), 3 functional SMXL subclades have been identified: SMAX1/SMXL2, SMXL345, and SMXL678. Of these, 2 subclades ensure endogenous phytohormone signal transduction. SMAX1/SMXL2 proteins are involved in KAI2 ligand (KL) signaling, while SMXL678 proteins are involved in strigolactone (SL) signaling. Many questions remain regarding the mode of action of these proteins, as well as their ancestral roles. We addressed these questions by investigating the functions of the 4 SMXL genes in the moss Physcomitrium patens. We demonstrate that PpSMXL proteins are involved in the conserved ancestral MAX2-dependent KL signaling pathway and negatively regulate growth. However, PpSMXL proteins expressed in Arabidopsis cannot replace SMAX1 or SMXL2 function in KL signaling, whereas they can functionally replace SMXL4 and SMXL5 and restore root growth. Therefore, the molecular functions of SMXL proteins are conserved, but their interaction networks are not. Moreover, the PpSMXLC/D clade positively regulates SL signal transduction in P. patens. Overall, our data reveal that SMXL proteins in moss mediate crosstalk between the SL and KL signaling pathways.
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Affiliation(s)
- Ambre Guillory
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Mauricio Lopez-Obando
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
- Institut de biologie moléculaire des plantes (IBMP), CNRS, University of Strasbourg, 12 rue du Général Zimmer, 67000 Strasbourg, France
| | - Khalissa Bouchenine
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Philippe Le Bris
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Alain Lécureuil
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Jean-Paul Pillot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Vincent Steinmetz
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - François-Didier Boyer
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Catherine Rameau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Alexandre de Saint Germain
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Sandrine Bonhomme
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
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Chen M, Dai Y, Liao J, Wu H, Lv Q, Huang Y, Liu L, Feng Y, Lv H, Zhou B, Peng D. TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2214-2234. [PMID: 38195092 DOI: 10.1093/jxb/erae005] [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: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.
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Affiliation(s)
- Min Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yani Dai
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Jiamin Liao
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Huan Wu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Huang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Lichang Liu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Yu Feng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Hongxuan Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, 410004, Changsha, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, 438107, Huaihua, Hunan, China
- Forestry Biotechnology Hunan Key Laboratories, Hunan, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, 410004, Changsha, Hunan, China
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7
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Li Q, Yu H, Chang W, Chang S, Guzmán M, Faure L, Wallner ES, Yan H, Greb T, Wang L, Yao R, Nelson DC. SMXL5 attenuates strigolactone signaling in Arabidopsis thaliana by inhibiting SMXL7 degradation. MOLECULAR PLANT 2024; 17:631-647. [PMID: 38475994 DOI: 10.1016/j.molp.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/10/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
Hormone-activated proteolysis is a recurring theme of plant hormone signaling mechanisms. In strigolactone signaling, the enzyme receptor DWARF14 (D14) and an F-box protein, MORE AXILLARY GROWTH2 (MAX2), mark SUPPRESSOR OF MAX2 1-LIKE (SMXL) family proteins SMXL6, SMXL7, and SMXL8 for rapid degradation. Removal of these transcriptional corepressors initiates downstream growth responses. The homologous proteins SMXL3, SMXL4, and SMXL5, however, are resistant to MAX2-mediated degradation. We discovered that the smxl4 smxl5 mutant has enhanced responses to strigolactone. SMXL5 attenuates strigolactone signaling by interfering with AtD14-SMXL7 interactions. SMXL5 interacts with AtD14 and SMXL7, providing two possible ways to inhibit SMXL7 degradation. SMXL5 function is partially dependent on an ethylene-responsive-element binding-factor-associated amphiphilic repression (EAR) motif, which typically mediates interactions with the TOPLESS family of transcriptional corepressors. However, we found that loss of the EAR motif reduces SMXL5-SMXL7 interactions and the attenuation of strigolactone signaling by SMXL5. We hypothesize that integration of SMXL5 into heteromeric SMXL complexes reduces the susceptibility of SMXL6/7/8 proteins to strigolactone-activated degradation and that the EAR motif promotes the formation or stability of these complexes. This mechanism may provide a way to spatially or temporally fine-tune strigolactone signaling through the regulation of SMXL5 expression or translation.
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Affiliation(s)
- Qingtian Li
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Yazhouwan National Laboratory, Sanya 572025, China; Hainan Seed Industry Laboratory, Sanya 57205, China.
| | - Haiyang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Wenwen Chang
- Key Laboratory of Seed Innovation, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sunhyun Chang
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Michael Guzmán
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Lionel Faure
- School of the Sciences, Biology Division, Texas Woman's University, Denton, TX 76204, USA
| | - Eva-Sophie Wallner
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Heqin Yan
- Yazhouwan National Laboratory, Sanya 572025, China
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Lei Wang
- Key Laboratory of Seed Innovation, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China.
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
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Fang P, Li M, Guo Q, Wu X, Hu Y, Cheng Y, Xu P. Genome-wide analysis of the SMXL gene family in common bean and identification of karrikin-responsive PvSMXL2 as a negative regulator of PEG-induced drought stress. Gene 2023; 887:147741. [PMID: 37634881 DOI: 10.1016/j.gene.2023.147741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/05/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is a major legume crop worldwide, but its growth and development frequently face challenges due to abiotic stresses, particularly drought. Proper supplement of copper could mitigate the adverse effects of drought, but excessive accumulation of this metal in plants can be harmful. The suppressor of MAX2 1-like (SMXL) gene family, which plays important roles in various plant processes, including stress responses, remains poorly understood in common bean. In this study, we identified nine orthologues of SMXL genes in common bean, which are located on six chromosomes and classified into four subgroups. Basic molecular properties, including theoretical isoelectric point (PI), molecular weight (MW), grand average of hydropathicity (GVIO), gene structure, and conserved motifs were characterized, and numerous cis-elements in promoters were predicted. The expression patterns of PvSMXL genes were found to be distinct under 10% polyethylene glycol (PEG)-induced drought stress and 200 μM Cu treatments. Most PvSMXLs showed reduced expression in response to Cu treatment, whereas nearly half PvSMXLs exhibited inducible expression under drought stress. PvSMXL2, which exhibited a rapid response to karrikin 1 (KAR1), an active form of the plant growth regulators newly found in the smoke of burning plant material, was down-regulated by both PEG-induced drought and Cu stresses. Transient silencing of PvSMXL2 resulted in enhanced drought stress tolerance without conferring Cu tolerance. These findings provide valuable insights into the functions of SMXL genes in common bean under abiotic stress conditions.
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Affiliation(s)
- Pingping Fang
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Minxuan Li
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Qinwei Guo
- Quzhou Key Laboratory for Germplasm Innovation and Utilization of Crop, Institute of Vegetables, Quzhou Academy of Agricultural and Forestry Sciences, Quzhou 324000, PR China
| | - Xinyang Wu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Yannan Hu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Yusu Cheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Pei Xu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China.
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9
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Ni F, Shah FA, Ren J. Identification and characterization of the karrikins signaling gene SsSMAX1 in Sapium sebiferum. PeerJ 2023; 11:e16610. [PMID: 38089914 PMCID: PMC10712317 DOI: 10.7717/peerj.16610] [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: 05/31/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
SUPPRESSOR OF MAX2 LIKE 1 (SMAX1) is a member of the SUPPRESSOR of MAX2 1‑LIKE family of genes and is known as a target protein of KARRIKIN INSENSITIVE2 (KAI2)-MORE AXILLARY BRANCHES2 (MAX2), which mediates karrikin signaling in Arabidopsis. SMAX1 plays a significant role in seed germination, hypocotyl elongation, and root hair development in Arabidopsis. SMAX1 has not yet been identified and characterized in woody plants. This study identified and characterized SsSMAX1 in Sapium sebiferum and found that SsSMAX1 was highly expressed in the seed, hypocotyl, and root tips of S. sebiferum. SsSMAX1 was functionally characterized by ectopic expression in Arabidopsis. SsSMAX1 overexpression lines of Arabidopsis showed significantly delayed seed germination and produced seedlings with longer hypocotyl and roots than wild-type and Atsmax1 functional mutants. SsSMAX1 overexpression lines of Arabidopsis also had broader and longer leaves and petioles than wild-type and Atsmax1, suggesting that SsSMAX1 is functionally conserved. This study characterizes the SMAX1 gene in a woody and commercially valuable bioenergy plant, Sapium sebiferum. The results of this study are beneficial to future research on the molecular biology of woody plants.
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Affiliation(s)
- Fang Ni
- Anhui Wenda University of Information Engineering, Hefei, Anhui, China
| | - Faheem Afzal Shah
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Jie Ren
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
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10
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Kułak K, Wojciechowska N, Samelak-Czajka A, Jackowiak P, Bagniewska-Zadworna A. How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis. PLANT METHODS 2023; 19:129. [PMID: 37981669 PMCID: PMC10659056 DOI: 10.1186/s13007-023-01109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues.
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Affiliation(s)
- Karolina Kułak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Natalia Wojciechowska
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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11
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Basso MF, Contaldi F, Lo Celso F, Baratto CM, Grossi-de-Sa MF, Barone G, Ferrante A, Martinelli F. Identification and expression profile of the SMAX/SMXL family genes in chickpea and lentil provide important players of biotechnological interest involved in plant branching. PLANTA 2023; 259:1. [PMID: 37966555 PMCID: PMC10651550 DOI: 10.1007/s00425-023-04277-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/28/2023] [Indexed: 11/16/2023]
Abstract
MAIN CONCLUSION SMAX/SMXL family genes were successfully identified and characterized in the chickpea and lentil and gene expression data revealed several genes associated with the modulation of plant branching and powerful targets for use in transgenesis and genome editing. Strigolactones (SL) play essential roles in plant growth, rooting, development, and branching, and are associated with plant resilience to abiotic and biotic stress conditions. Likewise, karrikins (KAR) are "plant smoke-derived molecules" that act in a hormonal signaling pathway similar to SL playing an important role in seed germination and hairy root elongation. The SMAX/SMXL family genes are part of these two signaling pathways, in addition to some of these members acting in a still little known SL- and KAR-independent signaling pathway. To date, the identification and functional characterization of the SMAX/SMXL family genes has not been performed in the chickpea and lentil. In this study, nine SMAX/SMXL genes were systematically identified and characterized in the chickpea and lentil, and their expression profiles were explored under different unstressless or different stress conditions. After a comprehensive in silico characterization of the genes, promoters, proteins, and protein-protein interaction network, the expression profile for each gene was determined using a meta-analysis from the RNAseq datasets and complemented with real-time PCR analysis. The expression profiles of the SMAX/SMXL family genes were very dynamic in different chickpea and lentil organs, with some genes assuming a tissue-specific expression pattern. In addition, these genes were significantly modulated by different stress conditions, indicating that SMAX/SMXL genes, although working in three distinct signaling pathways, can act to modulate plant resilience. Most CaSMAX/SMXL and partner genes such as CaTiE1 and CaLAP1, have a positive correlation with the plant branching level, while most LcSMAX/SMXL genes were less correlated with the plant branching level. The SMXL6, SMXL7, SMXL8, TiE1, LAP1, BES1, and BRC1 genes were highlighted as powerful targets for use in transgenesis and genome editing aiming to develop chickpea and lentil cultivars with improved architecture. Therefore, this study presented a detailed characterization of the SMAX/SMXL genes in the chickpea and lentil, and provided new insights for further studies focused on each SMAX/SMXL gene.
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Affiliation(s)
| | - Felice Contaldi
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Fabrizio Lo Celso
- Department of Physics and Chemical, University of Palermo, Viale Delle Scienze, Edificio 17, 90128, Palermo, Italy
| | - César Milton Baratto
- University of Western Santa Catarina, Biotechnological Center, UNOESC, Videira, SC, 89566-252, Brazil
| | | | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale Delle Scienze, Edificio 17, 90128, Palermo, Italy
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, University of Milan, Via Festa del Perdono, 20122, Milan, Italy
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
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12
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Basso MF, Contaldi F, Celso FL, Karalija E, Paz-Carrasco LC, Barone G, Ferrante A, Martinelli F. Expression profile of the NCED/CCD genes in chickpea and lentil during abiotic stress reveals a positive correlation with increased plant tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111817. [PMID: 37562731 DOI: 10.1016/j.plantsci.2023.111817] [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: 03/23/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Carotenoid cleavage dioxygenase (CCD) gene family is organized in two subfamilies: (i) 9-cis epoxycarotenoid dioxygenase (NCED) genes and (ii) CCD genes. NCED genes are essential for catalyzing the first step of the abscisic-acid (ABA) biosynthesis, while CCD genes produce precursors of the strigolactones hormone. The functional characterization of these gene subfamilies has not been yet performed in chickpea and lentil. Herein, were identified and systematically characterized two NCED and five CCD genes in the chickpea and two NCED and six CCD genes in lentil. After in silico sequence analysis and phylogeny, the expression profile of the NCED/CCD genes was determined by meta-analysis and real-time PCR in plants under different stress conditions. Sequence data revealed that NCED/CCD genes are highly conserved between chickpea and lentil. This conservation was observed both at gene and protein sequence levels and phylogenetic relationships. Analysis of the promoter sequences revealed that all NCED/CCD genes have a considerable number of cis-regulatory elements responsive to biotic and abiotic stress. Protein sequence analysis evidenced that NCED/CCD genes share several conserved motifs and that they have a highly interconnected interaction network. Furthermore, the three-dimensional structure of these proteins was determined and indicated that some proteins have structures with considerable similarity. The meta-analysis revealed that NCED/CCD genes are dynamically modulated in different organs and under different stress conditions, but they have a positive correlation with plant tolerance. In accordance, real-time PCR data showed that both NCED and CCD genes are differentially modulated in plants under drought stress. In particular, CaNCED2, CaCCD5, LcNCED2, LcCCD1, and LcCCD2 genes have a positive correlation with improved plant tolerance to drought stress. Therefore, this study presented a detailed characterization of the chickpea and lentil NCED/CCD genes and provided new insights to improve abiotic stress tolerance in these two important crops.
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Affiliation(s)
- Marcos Fernando Basso
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy; University of Western Santa Catarina, Biotechnological Center, UNOESC, Videira, SC 89566-252, Brazil
| | - Felice Contaldi
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy
| | - Fabrizio Lo Celso
- Department of Physics and Chemical, University of Palermo, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | - Erna Karalija
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy; Department of Biology, Faculty of science, University of Sarajevo, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina
| | - Lenin Celiano Paz-Carrasco
- National Institute of Agricultural Research (INIAP), Plant Pathology Department and Rice Breeding Program, Km 26 vía Duran-Tambo, Yaguachi, Guayas, Ecuador
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy.
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13
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Wang X, Mäkilä R, Mähönen AP. From procambium patterning to cambium activation and maintenance in the Arabidopsis root. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102404. [PMID: 37352651 DOI: 10.1016/j.pbi.2023.102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/08/2023] [Accepted: 05/20/2023] [Indexed: 06/25/2023]
Abstract
In addition to primary growth, which elongates the plant body, many plant species also undergo secondary growth to thicken their body. During primary vascular development, a subset of the vascular cells, called procambium and pericycle, remain undifferentiated to later gain vascular cambium and cork cambium identity, respectively. These two cambia are the lateral meristems providing secondary growth. The vascular cambium produces secondary xylem and phloem, which give plants mechanical support and transport capacity. Cork cambium produces a protective layer called cork. In this review, we focus on recent advances in understanding the formation of procambium and its gradual maturation to active cambium in the Arabidopsis thaliana root.
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Affiliation(s)
- Xin Wang
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Riikka Mäkilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ari Pekka Mähönen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
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14
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Yuan G, Lian Y, Wang J, Yong T, Gao H, Wu H, Yang T, Wang C. AtHSPR functions in gibberellin-mediated primary root growth by interacting with KNAT5 and OFP1 in Arabidopsis. PLANT CELL REPORTS 2023; 42:1629-1649. [PMID: 37597006 DOI: 10.1007/s00299-023-03057-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/02/2023] [Indexed: 08/21/2023]
Abstract
KEY MESSAGE AtHSPR forms a complex with KNAT5 and OFP1 to regulate primary root growth through GA-mediated root meristem activity. KNAT5-OFP1 functions as a negative regulator of AtHSPR in response to GA. Plant root growth is modulated by gibberellic acid (GA) signaling and depends on root meristem maintenance. ARABIDOPSIS THALIANA HEAT SHOCK PROTEIN-RELATED (AtHSPR) is a vital regulator of flowering time and salt stress tolerance. However, little is known about the role of AtHSPR in the regulation of primary root growth. Here, we report that athspr mutant exhibits a shorter primary root compared to wild type and that AtHSPR interacts with KNOTTED1-LIKE HOMEOBOX GENE 5 (KNAT5) and OVATE FAMILY PROTEIN 1 (OFP1). Genetic analysis showed that overexpression of KNAT5 or OFP1 caused a defect in primary root growth similar to that of the athspr mutant, but knockout of KNAT5 or OFP1 rescued the short root phenotype in the athspr mutant by altering root meristem activity. Further investigation revealed that KNAT5 interacts with OFP1 and that AtHSPR weakens the inhibition of GIBBERELLIN 20-OXIDASE 1 (GA20ox1) expression by the KNAT5-OFP1 complex. Moreover, root meristem cell proliferation and root elongation in 35S::KNAT5athspr and 35S::OFP1athspr seedlings were hypersensitive to GA3 treatment compared to the athspr mutant. Together, our results demonstrate that the AtHSPR-KNAT5-OFP1 module regulates root growth and development by impacting the expression of GA biosynthetic gene GA20ox1, which could be a way for plants to achieve plasticity in response to the environment.
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Affiliation(s)
- Guoqiang Yuan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuke Lian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Junmei Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Taibi Yong
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huanhuan Gao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Haijun Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tao Yang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Chongying Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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15
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Wallner ES, Dolan L, Bergmann DC. Arabidopsis stomatal lineage cells establish bipolarity and segregate differential signaling capacity to regulate stem cell potential. Dev Cell 2023; 58:1643-1656.e5. [PMID: 37607546 DOI: 10.1016/j.devcel.2023.07.024] [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: 02/14/2023] [Revised: 04/04/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023]
Abstract
Cell polarity combined with asymmetric cell divisions (ACDs) generates cellular diversity. In the Arabidopsis stomatal lineage, a single cortical polarity domain marked by BASL orients ACDs and is segregated to the larger daughter to enforce cell fate. We discovered a second, oppositely positioned polarity domain defined by OCTOPUS-LIKE (OPL) proteins, which forms prior to ACD and is segregated to the smaller (meristemoid) daughter. Genetic and misexpression analyses show that OPLs promote meristemoid-amplifying divisions and delay stomatal fate progression. Polarity mediates OPL segregation into meristemoids but is not required for OPL function. OPL localization and activity are largely independent of other stomatal polarity genes and of the brassinosteroid signaling components associated with OPLs in other contexts. While OPLs are unique to seed plants, ectopic expression in the liverwort Marchantia suppressed epidermal fate progression, suggesting that OPLs engage ancient and broadly conserved pathways to regulate cell division and cell fate.
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Affiliation(s)
- Eva-Sophie Wallner
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Gregor Mendel Institute, Dr.-Bohr-Gasse 3, 1030 Wien, Austria; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
| | - Liam Dolan
- Gregor Mendel Institute, Dr.-Bohr-Gasse 3, 1030 Wien, Austria
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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16
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Song X, Guo P, Xia K, Wang M, Liu Y, Chen L, Zhang J, Xu M, Liu N, Yue Z, Xu X, Gu Y, Li G, Liu M, Fang L, Deng XW, Li B. Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. Proc Natl Acad Sci U S A 2023; 120:e2310163120. [PMID: 37703282 PMCID: PMC10515167 DOI: 10.1073/pnas.2310163120] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/09/2023] [Indexed: 09/15/2023] Open
Abstract
Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the shoot regeneration process in crop callus remains largely elusive. This study pioneers the exploration of the spatial transcriptome of tomato callus during shoot regeneration. The findings reveal the presence of highly heterogeneous cell populations within the callus, including epidermis, vascular tissue, shoot primordia, inner callus, and outgrowth shoots. By characterizing the spatially resolved molecular features of shoot primordia and surrounding cells, specific factors essential for shoot primordia formation are identified. Notably, chlorenchyma cells, enriched in photosynthesis-related processes, play a crucial role in promoting shoot primordia formation and subsequent shoot regeneration. Light is shown to promote shoot regeneration by inducing chlorenchyma cell development and coordinating sugar signaling. These findings significantly advance our understanding of the cellular and molecular aspects of shoot regeneration in tomato callus and demonstrate the immense potential of spatial transcriptomics in plant biology.
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Affiliation(s)
- Xiehai Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Pengru Guo
- Beijing Genomics Institute Research, Beijing102601, China
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Keke Xia
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Meiling Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Yongqi Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Lichuan Chen
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Jinhui Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Mengyuan Xu
- Beijing Genomics Institute Research, Beijing102601, China
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Naixu Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Zhiliang Yue
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Xun Xu
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Ying Gu
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong271018, China
| | - Min Liu
- Baimaike Intelligent Manufacturing, Qingdao, Shandong266500, China
| | - Liang Fang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong518005, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
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17
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Kodama K, Xie X, Kyozuka J. The D14 and KAI2 Orthologs of Gymnosperms Sense Strigolactones and KL Mimics, Respectively, and the Signals Are Transduced to Control Downstream Genes. PLANT & CELL PHYSIOLOGY 2023; 64:1057-1065. [PMID: 37489639 DOI: 10.1093/pcp/pcad072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/21/2023] [Accepted: 07/02/2023] [Indexed: 07/26/2023]
Abstract
Strigolactones (SLs), lactone-containing carotenoid derivatives, function as signaling molecules in the rhizosphere, inducing symbiosis with arbuscular mycorrhizal. In addition, as a class of plant hormones, SLs control plant growth and development in flowering plants (angiosperms). Recent studies show that the ancestral function of SLs, which precede terrestrialization of plants, is as rhizosphere signaling molecules. SLs were then recruited as a class of plant hormones through the step-by-step acquisition of signaling components. The D14 gene encoding the SL receptor arose by gene duplication of KARRIKIN INSENSITIVE2 (KAI2), the receptor of karrikins and KAI2 ligand (KL), an unknown ligand, in the common ancestor of seed plants. KL signaling targets SMAX1, a repressor protein. On the other hand, the SL signaling targets SMXL78 subclade repressors, which arose by duplication of SMAX1 in angiosperms. Thus, gymnosperms contain the SL receptor D14 but not SMXL78, the SL signaling-specific repressor proteins. We studied two gymnosperm species, ginkgo (Ginkgo biloba) and Japanese umbrella pine (Sciadopitys verticillata), to clarify whether SLs are perceived and the signals are transduced in gymnosperms. We show that D14 and KAI2 of ginkgo and Japanese umbrella pine specifically perceive an SL analog and KL mimic, respectively. Furthermore, our results suggest that both SL signaling and KL signaling target SMAX1, and the specific localization of the receptor may result in the specificity of the signaling in gymnosperms.
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Affiliation(s)
- Kyoichi Kodama
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577 Japan
| | - Xiaonan Xie
- Center for Bioscience Research and Education, Utsunomiya University, 350 Minemachi, Utsunomiya, Tochigi, 321-8505 Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577 Japan
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18
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Ma B, Zhu J, Huang X. Diversification of plant SUPPRESSOR OF MAX2 1 (SMAX1)-like genes and genome-wide identification and characterization of cotton SMXL gene family. BMC PLANT BIOLOGY 2023; 23:419. [PMID: 37691127 PMCID: PMC10494346 DOI: 10.1186/s12870-023-04421-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Strigolactones (SLs) are a recently discovered class of plant hormones. SUPPRESSOR OF MAX2 1 (SMAX1)-like proteins, key component of the SL signaling pathway, have been studied extensively for their roles in regulating plant growth and development, such as plant branching. However, systematic identification and functional characterization of SMXL genes in cotton (Gossypium sp.), an important fiber and oil crop, has rarely been conducted. RESULTS We identified 210 SMXL genes from 21 plant genomes and examined their evolutionary relationships. The structural characteristics of the SMXL genes and their encoded proteins exhibited both consistency and diversity. All plant SMXL proteins possess a conserved Clp-N domain, P-loop NTPase, and EAR motif. We identified 63 SMXL genes in cotton and classified these into four evolutionary branches. Gene expression analysis revealed tissue-specific expression patterns of GhSMXL genes, with some upregulated in response to GR24 treatment. Protein co-expression network analysis showed that GhSMXL6, GhSMXL7-1, and GhSMXL7-2 mainly interact with proteins functioning in growth and development, while virus-induced gene silencing revealed that GhSMAX1-1 and GhSMAX1-2 suppress the growth and development of axillary buds. CONCLUSIONS SMXL gene family members show evolutionary diversification through the green plant lineage. GhSMXL6/7-1/7-2 genes play critical roles in the SL signaling pathway, while GhSMXL1-1 and GhSMXL1-2 function redundantly in growth of axillary buds. Characterization of the cotton SMXL gene family provides new insights into their roles in responding to SL signals and in plant growth and development. Genes identified in this study could be used as the candidate genes for improvement of plant architecture and crop yield.
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Affiliation(s)
- Bin Ma
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China
| | - Jianbo Zhu
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China.
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19
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Seo PJ, Lee HG, Choi HY, Lee S, Park CM. Complexity of SMAX1 signaling during seedling establishment. TRENDS IN PLANT SCIENCE 2023; 28:902-912. [PMID: 37069002 DOI: 10.1016/j.tplants.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/12/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Karrikins (KARs) are small butenolide compounds identified in the smoke of burning vegetation. Along with the stimulating effects on seed germination, KARs also regulate seedling vigor and adaptive behaviors, such as seedling morphogenesis, root hair development, and stress acclimation. The pivotal KAR signaling repressor, SUPPRESSOR OF MAX2 1 (SMAX1), plays central roles in these developmental and morphogenic processes through an extensive signaling network that governs seedling responses to endogenous and environmental cues. Here, we summarize the versatile roles of SMAX1 reported in recent years and discuss how SMAX1 integrates multiple growth hormone signals into optimizing seedling establishment. We also discuss the evolutionary relevance of the SMAX1-mediated signaling pathways during the colonization of aqueous plants to terrestrial environments.
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Affiliation(s)
- Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Hye-Young Choi
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sangmin Lee
- Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
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20
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Pandey SS, Xu J, Achor DS, Li J, Wang N. Microscopic and Transcriptomic Analyses of Early Events Triggered by ' Candidatus Liberibacter asiaticus' in Young Flushes of Huanglongbing-Positive Citrus Trees. PHYTOPATHOLOGY 2023; 113:985-997. [PMID: 36449527 DOI: 10.1094/phyto-10-22-0360-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
'Candidatus Liberibacter asiaticus' (CLas) is associated with the devastating citrus disease Huanglongbing (HLB). Young flushes are the center of the HLB pathosystem due to their roles in the psyllid life cycle and in the acquisition and transmission of CLas. However, the early events of CLas infection and how CLas modulates young flush physiology remain poorly understood. Here, transmission electron microscopy analysis showed that the mean diameter of the sieve pores decreased in young leaves of HLB-positive trees after CLas infection, consistent with CLas-triggered callose deposition. RNA-seq-based global expression analysis of young leaves of HLB-positive sweet orange with (CLas-Pos) and without (CLas-Neg) detectable CLas demonstrated a significant impact on gene expression in young leaves, including on the expression of genes involved in host immunity, stress response, and plant hormone biosynthesis and signaling. CLas-Pos and CLas-Neg expression data displayed distinct patterns. The number of upregulated genes was higher than that of the downregulated genes in CLas-Pos for plant-pathogen interactions, glutathione metabolism, peroxisome, and calcium signaling, which are commonly associated with pathogen infections, compared with the healthy control. On the contrary, the number of upregulated genes was lower than that of the downregulated genes in CLas-Neg for genes involved in plant-pathogen interactions and peroxisome biogenesis/metabolism. Additionally, a time-course quantitative reverse transcription-PCR-based expression analysis visualized the induced expression of companion cell-specific genes, phloem protein 2 genes, and sucrose transport genes in young flushes triggered by CLas. This study advances our understanding of early events during CLas infection of citrus young flushes.
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Affiliation(s)
- Sheo Shankar Pandey
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Diann S Achor
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850
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21
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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22
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Hardtke CS. Phloem development. THE NEW PHYTOLOGIST 2023. [PMID: 37243530 DOI: 10.1111/nph.19003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/13/2023] [Indexed: 05/29/2023]
Abstract
The evolution of the plant vascular system is a key process in Earth history because it enabled plants to conquer land and transform the terrestrial surface. Among the vascular tissues, the phloem is particularly intriguing because of its complex functionality. In angiosperms, its principal components are the sieve elements, which transport phloem sap, and their neighboring companion cells. Together, they form a functional unit that sustains sap loading, transport, and unloading. The developmental trajectory of sieve elements is unique among plant cell types because it entails selective organelle degradation including enucleation. Meticulous analyses of primary, so-called protophloem in the Arabidopsis thaliana root meristem have revealed key steps in protophloem sieve element formation at single-cell resolution. A transcription factor cascade connects specification with differentiation and also orchestrates phloem pole patterning via noncell-autonomous action of sieve element-derived effectors. Reminiscent of vascular tissue patterning in secondary growth, these involve receptor kinase pathways, whose antagonists guide the progression of sieve element differentiation. Receptor kinase pathways may also safeguard phloem formation by maintaining the developmental plasticity of neighboring cell files. Our current understanding of protophloem development in the A. thaliana root has reached sufficient detail to instruct molecular-level investigation of phloem formation in other organs.
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Affiliation(s)
- Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, CH-1015, Lausanne, Switzerland
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23
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Wallner ES, Tonn N, Shi D, Luzzietti L, Wanke F, Hunziker P, Xu Y, Jung I, Lopéz-Salmerón V, Gebert M, Wenzl C, Lohmann JU, Harter K, Greb T. OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module driving phloem development. Nat Commun 2023; 14:2128. [PMID: 37059727 PMCID: PMC10104830 DOI: 10.1038/s41467-023-37790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Spatial specificity of cell fate decisions is central for organismal development. The phloem tissue mediates long-distance transport of energy metabolites along plant bodies and is characterized by an exceptional degree of cellular specialization. How a phloem-specific developmental program is implemented is, however, unknown. Here we reveal that the ubiquitously expressed PHD-finger protein OBE3 forms a central module with the phloem-specific SMXL5 protein for establishing the phloem developmental program in Arabidopsis thaliana. By protein interaction studies and phloem-specific ATAC-seq analyses, we show that OBE3 and SMXL5 proteins form a complex in nuclei of phloem stem cells where they promote a phloem-specific chromatin profile. This profile allows expression of OPS, BRX, BAM3, and CVP2 genes acting as mediators of phloem differentiation. Our findings demonstrate that OBE3/SMXL5 protein complexes establish nuclear features essential for determining phloem cell fate and highlight how a combination of ubiquitous and local regulators generate specificity of developmental decisions in plants.
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Affiliation(s)
- Eva-Sophie Wallner
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
- Gilbert Biological Sciences, Stanford University, Stanford, CA, 94305-5020, USA
| | - Nina Tonn
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Dongbo Shi
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
- Japan RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, 14476, Germany
- Japan Science and Technology Agency (JST), Saitama, Kawaguchi, Japan
| | - Laura Luzzietti
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Friederike Wanke
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Pascal Hunziker
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Yingqiang Xu
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Ilona Jung
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Vadir Lopéz-Salmerón
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
- BD Bioscience, 69126, Heidelberg, Germany
| | - Michael Gebert
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Christian Wenzl
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Jan U Lohmann
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany.
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24
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Waters MT, Nelson DC. Karrikin perception and signalling. THE NEW PHYTOLOGIST 2023; 237:1525-1541. [PMID: 36333982 DOI: 10.1111/nph.18598] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Karrikins (KARs) are a class of butenolide compounds found in smoke that were first identified as seed germination stimulants for fire-following species. Early studies of KARs classified the germination and postgermination responses of many plant species and investigated crosstalk with plant hormones that regulate germination. The discovery that Arabidopsis thaliana responds to KARs laid the foundation for identifying mutants with altered KAR responses. Genetic analysis of KAR signalling revealed an unexpected link to strigolactones (SLs), a class of carotenoid-derived plant hormones. Substantial progress has since been made towards understanding how KARs are perceived and regulate plant growth, in no small part due to advances in understanding SL perception. KAR and SL signalling systems are evolutionarily related and retain a high degree of similarity. There is strong evidence that KARs are natural analogues of an endogenous signal(s), KAI2 ligand (KL), which remains unknown. KAR/KL signalling regulates many developmental processes in plants including germination, seedling photomorphogenesis, and root and root hair growth. KAR/KL signalling also affects abiotic stress responses and arbuscular mycorrhizal symbiosis. Here, we summarise the current knowledge of KAR/KL signalling and discuss current controversies and unanswered questions in this field.
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Affiliation(s)
- Mark T Waters
- School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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25
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Zheng X, Liu F, Yang X, Li W, Chen S, Yue X, Jia Q, Sun X. The MAX2-KAI2 module promotes salicylic acid-mediated immune responses in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36738234 DOI: 10.1111/jipb.13463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Arabidopsis MORE AXILLARY GROWTH2 (MAX2) is a key component in the strigolactone (SL) and karrikin (KAR) signaling pathways and regulates the degradation of SUPPRESSOR OF MAX2 1/SMAX1-like (SMAX1/SMXL) proteins, which are transcriptional co-repressors that regulate plant architecture, as well as abiotic and biotic stress responses. The max2 mutation reduces resistance against Pseudomonas syringae pv. tomato (Pst). To uncover the mechanism of MAX2-mediated resistance, we evaluated the resistance of various SL and KAR signaling pathway mutants. The resistance of SL-deficient mutants and of dwarf 14 (d14) was similar to that of the wild-type, whereas the resistance of the karrikin insensitive 2 (kai2) mutant was compromised, demonstrating that the KAR signaling pathway, not the SL signaling pathway, positively regulates the immune response. We measured the resistance of smax1 and smxl mutants, as well as the double, triple, and quadruple mutants with max2, which revealed that both the smax1 mutant and smxl6/7/8 triple mutant rescue the low resistance phenotype of max2 and that SMAX1 accumulation diminishes resistance. The susceptibility of smax1D, containing a degradation-insensitive form of SMAX1, further confirmed the SMAX1 function in the resistance. The relationship between the accumulation of SMAX1/SMXLs and disease resistance suggested that the inhibitory activity of SMAX1 to resistance requires SMXL6/7/8. Moreover, the exogenous application of KAR2 enhanced resistance against Pst, but KAR-induced resistance depended on salicylic acid (SA) signaling. Inhibition of karrikin signaling delayed SA-mediated defense responses and inhibited pathogen-induced protein biosynthesis. Together, we propose that the MAX2-KAI2-SMAX1 complex regulates resistance with the assistance of SMXL6/7/8 and SA signaling and that SMAX1/SMXLs possibly form a multimeric complex with their target transcription factors to fine tune immune responses.
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Affiliation(s)
- Xiujuan Zheng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Fangqian Liu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Xianfeng Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Weiqiang Li
- Jilin Da'an Agro-ecosystem National Observation Research Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Sique Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Xinwu Yue
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Qi Jia
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Xinli Sun
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
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26
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Ribeiro C, Xu J, Hendrich C, Pandey SS, Yu Q, Gmitter FG, Wang N. Seasonal Transcriptome Profiling of Susceptible and Tolerant Citrus Cultivars to Citrus Huanglongbing. PHYTOPATHOLOGY 2023; 113:286-298. [PMID: 36001783 DOI: 10.1094/phyto-05-22-0179-r] [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] [Indexed: 06/15/2023]
Abstract
Citrus huanglongbing (HLB) caused by 'Candidatus Liberibacter asiaticus' (CLas) is the most devastating citrus disease worldwide. Most commercial citrus cultivars are susceptible to HLB, with a few more tolerant exceptions such as 'LB8-9' Sugar Belle mandarin. Transcriptomic analyses have been widely used to investigate the potential mechanisms for disease susceptibility, resistance, or tolerance. Previous transcriptomic studies related to HLB mostly focused on single time point data collection. We hypothesize that changes in day length and temperature throughout the seasons have profound effects on citrus-CLas interactions. Here, we conducted RNA-seq analyses on HLB-susceptible Valencia sweet orange and HLB-tolerant mandarin 'LB8-9' in winter, spring, summer, and fall. Significant variations in differentially expressed genes (DEGs) related to HLB were observed among the four seasons. For both cultivars, the highest number of DEGs were found in the spring. CLas infection stimulates the expression of immune-related genes such as NBS-LRR, RLK, RLCK, CDPK, MAPK pathway, reactive oxygen species (ROS), and PR genes in both cultivars, consistent with the model that HLB is a pathogen-triggered immune disease. HLB-positive mandarin 'LB8-9' trees contained higher concentrations of maltose and sucrose, which are known to scavenge ROS. In addition, mandarin 'LB8-9' showed higher expression of genes involved in phloem regeneration, which might contribute to its HLB tolerance. This study shed light on the pathogenicity mechanism of the HLB pathosystem and the tolerance mechanism against HLB, providing valuable insights into HLB management.
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Affiliation(s)
- Camila Ribeiro
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Jin Xu
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Connor Hendrich
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Sheo Shankar Pandey
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Qibin Yu
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Frederick G Gmitter
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Nian Wang
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
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27
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Sidorenko A, Omelyanchuk N, Zemlyanskaya E. Molecular mechanisms of vascular tissue patterning in Arabidopsis thaliana L. roots. Vavilovskii Zhurnal Genet Selektsii 2022; 26:721-732. [PMID: 36694717 PMCID: PMC9834716 DOI: 10.18699/vjgb-22-88] [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: 09/16/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 01/06/2023] Open
Abstract
A vascular system in plants is a product of aromorphosis that enabled them to colonize land because it delivers water, mineral and organic compounds to plant organs and provides effective communications between organs and mechanical support. Vascular system development is a common object of fundamental research in plant development biology. In the model plant Arabidopsis thaliana, early stages of vascular tissue formation in the root are a bright example of the self-organization of a bisymmetric (having two planes of symmetry) pattern of hormone distribution, which determines vascular cell fates. In the root, vascular tissue development comprises four stages: (1) specification of progenitor cells for the provascular meristem in early embryonic stages, (2) the growth and patterning of the embryo provascular meristem, (3) postembryonic maintenance of the cell identity in the vascular tissue initials within the root apical meristem, and (4) differentiation of their descendants. Although the anatomical details of A. thaliana root vasculature development have long been known and described in detail, our knowledge of the underlying molecular and genetic mechanisms remains limited. In recent years, several important advances have been made, shedding light on the regulation of the earliest events in provascular cells specification. In this review, we summarize the latest data on the molecular and genetic mechanisms of vascular tissue patterning in A. thaliana root. The first part of the review describes the root vasculature ontogeny, and the second reconstructs the sequence of regulatory events that underlie this histogenesis and determine the development of the progenitors of the vascular initials in the embryo and organization of vascular initials in the seedling root.
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Affiliation(s)
- A.D. Sidorenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - N.A. Omelyanchuk
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E.V. Zemlyanskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
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28
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Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield. Biomolecules 2022; 12:biom12121772. [PMID: 36551200 PMCID: PMC9775962 DOI: 10.3390/biom12121772] [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: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the "source" and "sink" transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.
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29
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Genome-Wide Identification of SMXL Gene Family in Soybean and Expression Analysis of GmSMXLs under Shade Stress. PLANTS 2022; 11:plants11182410. [PMID: 36145811 PMCID: PMC9500757 DOI: 10.3390/plants11182410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022]
Abstract
SMXL6,7,8 are important target proteins in strigolactone (SL) signal pathway, which negatively regulate the reception and response of SL signal, and play an important role in regulating plant branching. However, there is a relative lack of research on soybean SMXL gene family. In this study, 31 soybean SMXL genes were identified by phylogenetic analysis and divided into three groups. Based on the analysis of GmSMXL gene’s structure and motif composition, it was found that the GmSMXL members in the same group were similar. The results of cis-element analysis showed that GmSMXL genes may regulate the growth and development of soybean by responding to hormones and environment. Based on the tissue specificity analysis and GR24 treatment, the results showed that four GmSMXLs in G1 group were predominantly expressed in stems, axillary buds and leaves and involved in SL signal pathway. Finally, under shading stress, the expression of four genes in G1 group was slightly different in different varieties, which may be the reason for the difference in branching ability of different varieties under shading stress. We have systematically studied the SMXL gene family in soybean, which may lay a foundation for the study of the function of GmSMXL gene in the future.
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30
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Qian P, Song W, Zaizen-Iida M, Kume S, Wang G, Zhang Y, Kinoshita-Tsujimura K, Chai J, Kakimoto T. A Dof-CLE circuit controls phloem organization. NATURE PLANTS 2022; 8:817-827. [PMID: 35817820 DOI: 10.1038/s41477-022-01176-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The phloem consists of sieve elements (SEs) and companion cells (CCs). Here we show that Dof-class transcription factors preferentially expressed in the phloem (phloem-Dofs) are not only necessary and sufficient for SE and CC differentiation, but also induce negative regulators of phloem development, CLAVATA3/EMBRYO SURROUNDING REGION-RELATED25 (CLE25), CLE26 and CLE45 secretory peptides. CLEs were perceived by BARELY ANY MERISTEM (BAM)-class receptors and CLAVATA3 INSENSITIVE RECEPTOR KINASE (CIK) co-receptors, and post-transcriptionally decreased phloem-Dof proteins and repressed SE and CC formation. Multiple mutations in CLE-, BAM- or CIK-class genes caused ectopic formation of SEs and CCs, producing an SE/CC cluster at each phloem region. We propose that while phloem-Dofs induce phloem cell formation, they inhibit excess phloem cell formation by inducing CLEs. Normal-positioned SE and CC precursor cells appear to overcome the effect of CLEs by reinforcing the production of phloem-Dofs through a positive feedback transcriptional regulation.
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Affiliation(s)
- Pingping Qian
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
| | - Wen Song
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
- Cluster of Excellence in Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Miki Zaizen-Iida
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
- Organismal and Evolutionary Biology Research Programme, Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Sawa Kume
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Guodong Wang
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ye Zhang
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | | | - Jijie Chai
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
- Cluster of Excellence in Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Tatsuo Kakimoto
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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31
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Haas AS, Shi D, Greb T. Cell Fate Decisions Within the Vascular Cambium-Initiating Wood and Bast Formation. FRONTIERS IN PLANT SCIENCE 2022; 13:864422. [PMID: 35548289 PMCID: PMC9082745 DOI: 10.3389/fpls.2022.864422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 06/15/2023]
Abstract
Precise coordination of cell fate decisions is a hallmark of multicellular organisms. Especially in tissues with non-stereotypic anatomies, dynamic communication between developing cells is vital for ensuring functional tissue organization. Radial plant growth is driven by a plant stem cell niche known as vascular cambium, usually strictly producing secondary xylem (wood) inward and secondary phloem (bast) outward, two important structures serving as much-needed CO2 depositories and building materials. Because of its bidirectional nature and its developmental plasticity, the vascular cambium serves as an instructive paradigm for investigating principles of tissue patterning. Although genes and hormones involved in xylem and phloem formation have been identified, we have a yet incomplete picture of the initial steps of cell fate transitions of stem cell daughters into xylem and phloem progenitors. In this mini-review perspective, we describe two possible scenarios of cell fate decisions based on the current knowledge about gene regulatory networks and how cellular environments are established. In addition, we point out further possible research directions.
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Affiliation(s)
- Aylin S. Haas
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Dongbo Shi
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
- RIKEN Center for Sustainable Resource Science (CSRS), Tsurumi-Yokohama, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Japan
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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32
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Shahan R, Hsu CW, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN, Ohler U. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Dev Cell 2022; 57:543-560.e9. [PMID: 35134336 DOI: 10.1101/2020.06.29.178863] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/27/2021] [Accepted: 01/13/2022] [Indexed: 05/22/2023]
Abstract
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.
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Affiliation(s)
- Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Che-Wei Hsu
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Benjamin J Cole
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Isaiah W Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Stephen Zhang
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anna Hendrika Cornelia Vlot
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany.
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Shahan R, Hsu CW, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN, Ohler U. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Dev Cell 2022; 57:543-560.e9. [PMID: 35134336 PMCID: PMC9014886 DOI: 10.1016/j.devcel.2022.01.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/27/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022]
Abstract
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model to investigate the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development. How do transcriptional networks regulate organ development? Using scRNA-seq, Shahan and Hsu et al. produced an Arabidopsis root atlas, revealing gradual gene expression changes underlying differentiation of cell types and candidate regulators of cell fate. The atlas enabled interpretation of smaller scRNA-seq datasets and revealed new phenotypes in developmental mutants.
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Affiliation(s)
- Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Che-Wei Hsu
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Benjamin J Cole
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Isaiah W Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Stephen Zhang
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Anna Hendrika Cornelia Vlot
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany.
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Aliaga Fandino AC, Hardtke CS. Auxin transport in developing protophloem: A case study in canalization. JOURNAL OF PLANT PHYSIOLOGY 2022; 269:153594. [PMID: 34953411 DOI: 10.1016/j.jplph.2021.153594] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/03/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Spatiotemporal cues orchestrate the development of organs and cellular differentiation in multicellular organisms. For instance, in the root apical meristem an auxin gradient patterns the transition from stem cell maintenance to transit amplification and eventual differentiation. Among the proximal tissues generated by this growth apex, the early, so-called protophloem, is the first tissue to differentiate. This observation has been linked to increased auxin activity in the developing protophloem sieve element cell files as compared to the neighboring tissues. Here we review recent progress in the characterization of the unique mechanism by which auxin canalizes its activity in the developing protophloem and fine-tunes its own transport to guide proper timing of protophloem sieve element differentiation.
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Affiliation(s)
- Ana Cecilia Aliaga Fandino
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.
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35
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Song C, Zhao J, Guichard M, Shi D, Grossmann G, Schmitt C, Jouannet V, Greb T. Strigo-D2-a bio-sensor for monitoring spatio-temporal strigolactone signaling patterns in intact plants. PLANT PHYSIOLOGY 2022; 188:97-110. [PMID: 34718781 PMCID: PMC8774841 DOI: 10.1093/plphys/kiab504] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/09/2021] [Indexed: 05/29/2023]
Abstract
Strigolactones (SLs) are a class of plant hormones that mediate biotic interactions and modulate developmental programs in response to endogenous and exogenous stimuli. However, a comprehensive view on the spatio-temporal pattern of SL signaling has not been established, and tools for a systematic in planta analysis do not exist. Here, we present Strigo-D2, a genetically encoded ratiometric SL signaling sensor that enables the examination of SL signaling distribution at cellular resolution and is capable of rapid response to altered SL levels in intact Arabidopsis (Arabidopsis thaliana) plants. By monitoring the abundance of a truncated and fluorescently labeled SUPPRESSOR OF MAX2 1-LIKE 6 (SMXL6) protein, a proteolytic target of the SL signaling machinery, we show that all cell types investigated have the capacity to respond to changes in SL levels but with very different dynamics. In particular, SL signaling is pronounced in vascular cells but low in guard cells and the meristematic region of the root. We also show that other hormones leave Strigo-D2 activity unchanged, indicating that initial SL signaling steps work in isolation from other hormonal signaling pathways. The specificity and spatio-temporal resolution of Strigo-D2 underline the value of the sensor for monitoring SL signaling in a broad range of biological contexts with highly instructive analytical depth.
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Affiliation(s)
- Changzheng Song
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Jiao Zhao
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Marjorie Guichard
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Dongbo Shi
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
- RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-Yokohama 230-0045, Japan
| | - Guido Grossmann
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christian Schmitt
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Virginie Jouannet
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
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Hu J, Hu X, Yang Y, He C, Hu J, Wang X. Strigolactone signaling regulates cambial activity through repression of WOX4 by transcription factor BES1. PLANT PHYSIOLOGY 2022; 188:255-267. [PMID: 34687296 PMCID: PMC8774819 DOI: 10.1093/plphys/kiab487] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
During secondary growth, meristematic cells in the cambium can either proliferate to maintain the stem cell population or differentiate into xylem or phloem. The balance between these two developmental trajectories is tightly regulated by many environmental and endogenous cues. Strigolactones (SLs), a class of plant hormones, were previously reported to regulate secondary growth by promoting cambium activity. However, the underlying molecular mechanisms of SL action in plant secondary growth are not well understood. We performed histological, genetic, and biochemical analyses using genetic materials in Arabidopsis (Arabidopsis thaliana) with altered activity of the transcription factors BRI1-EMS-SUPPRESSOR1 (BES1) or WUSCHEL-related HOMEOBOX4 (WOX4) or lacking MORE AXILLARY SHOOT2 (MAX2), a key positive component in the SL signaling pathway. We found that BES1, a downstream regulator in the SL signaling pathway that promotes shoot branching and xylem differentiation, also inhibits WOX4 expression, a key regulator of cambium cell division in the intercellular TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF)-TDIF RECEPTOR (TDR) signaling pathway. The antagonistic roles of BES1 and WOX4 in the regulation of cambium activity may integrate intercellular TDIF signals to efficiently and bidirectionally modulate cambium cell proliferation and differentiation. As both BES1 and WOX4 are widely involved in various endogenous signals and responses to environmental stimuli, these findings may provide insight into the dynamic regulation of cambium development.
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Affiliation(s)
- Jie Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China
| | - Xiaotong Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China
| | - Chunmei He
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China
| | - Jin Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China
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Temmerman A, Guillory A, Bonhomme S, Goormachtig S, Struk S. Masks Start to Drop: Suppressor of MAX2 1-Like Proteins Reveal Their Many Faces. FRONTIERS IN PLANT SCIENCE 2022; 13:887232. [PMID: 35645992 PMCID: PMC9133912 DOI: 10.3389/fpls.2022.887232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/25/2022] [Indexed: 05/11/2023]
Abstract
Although the main players of the strigolactone (SL) signaling pathway have been characterized genetically, how they regulate plant development is still poorly understood. Of central importance are the SUPPRESSOR OF MAX2 1-LIKE (SMXL) proteins that belong to a family of eight members in Arabidopsis thaliana, of which one subclade is involved in SL signaling and another one in the pathway of the chemically related karrikins. Through proteasomal degradation of these SMXLs, triggered by either DWARF14 (D14) or KARRIKIN INSENSITIVE2 (KAI2), several physiological processes are controlled, such as, among others, shoot and root architecture, seed germination, and seedling photomorphogenesis. Yet another clade has been shown to be involved in vascular development, independently of the D14 and KAI2 actions and not relying on proteasomal degradation. Despite their role in several aspects of plant development, the exact molecular mechanisms by which SMXLs regulate them are not completely unraveled. To fill the major knowledge gap in understanding D14 and KAI2 signaling, SMXLs are intensively studied, making it challenging to combine all the insights into a coherent characterization of these important proteins. To this end, this review provides an in-depth exploration of the recent data regarding their physiological function, evolution, structure, and molecular mechanism. In addition, we propose a selection of future perspectives, focusing on the apparent localization of SMXLs in subnuclear speckles, as observed in transient expression assays, which we couple to recent advances in the field of biomolecular condensates and liquid-liquid phase separation.
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Affiliation(s)
- Arne Temmerman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-Center for Plant Systems Biology, Ghent, Belgium
| | - Ambre Guillory
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Sandrine Bonhomme
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-Center for Plant Systems Biology, Ghent, Belgium
| | - Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-Center for Plant Systems Biology, Ghent, Belgium
- *Correspondence: Sylwia Struk,
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38
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Zhai N, Xu L. Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration. NATURE PLANTS 2021; 7:1453-1460. [PMID: 34782770 DOI: 10.1038/s41477-021-01015-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/05/2021] [Indexed: 05/12/2023]
Abstract
In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
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Affiliation(s)
- Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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39
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Bunsick M, McCullough R, McCourt P, Lumba S. Plant hormone signaling: Is upside down right side up? CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102070. [PMID: 34166978 DOI: 10.1016/j.pbi.2021.102070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/29/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Since the early days of plant biology, small molecule hormones have held a central place in our understanding of development. A key feature of plant hormone action is the ability to regulate multiple developmental processes. Despite this pleiotropy, decades of genetic and molecular studies have shown that plant hormone signaling is often canalized through a core pathway. This raises the difficult question of how one signaling pathway produces different outputs in different tissues. Drawing on examples from gibberellin and strigolactone signaling pathways, we propose this conceptual problem arises from an upside-down perspective of hormone signaling. Recent studies have revealed hormone and core pathway-independent mechanisms of regulating downstream signaling components, which could explain multiple developmental responses to the same hormone.
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Affiliation(s)
- Michael Bunsick
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, M5S 3B2, Canada
| | - Rachel McCullough
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, M5S 3B2, Canada
| | - Peter McCourt
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, M5S 3B2, Canada
| | - Shelley Lumba
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, M5S 3B2, Canada.
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40
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Li H, Testerink C, Zhang Y. How roots and shoots communicate through stressful times. TRENDS IN PLANT SCIENCE 2021; 26:940-952. [PMID: 33896687 DOI: 10.1016/j.tplants.2021.03.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/19/2021] [Accepted: 03/16/2021] [Indexed: 05/06/2023]
Abstract
When plants face an environmental stress such as water deficit, soil salinity, high temperature, or shade, good communication between above- and belowground organs is necessary to coordinate growth and development. Various signals including hormones, peptides, proteins, hydraulic signals, and metabolites are transported mostly through the vasculature to distant tissues. How shoots and roots synchronize their response to stress using mobile signals is an emerging field of research. We summarize recent advances on mobile signals regulating shoot stomatal movement and root development in response to highly localized environmental cues. In addition, we highlight how the vascular system is not only a conduit but is also flexible in its development in response to abiotic stress.
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Affiliation(s)
- Hongfei Li
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, The Netherlands.
| | - Yanxia Zhang
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, The Netherlands.
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41
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Lopez-Anido CB, Vatén A, Smoot NK, Sharma N, Guo V, Gong Y, Anleu Gil MX, Weimer AK, Bergmann DC. Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. Dev Cell 2021; 56:1043-1055.e4. [PMID: 33823130 DOI: 10.1016/j.devcel.2021.03.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 12/20/2022]
Abstract
Dynamic cell identities underlie flexible developmental programs. The stomatal lineage in the Arabidopsis leaf epidermis features asynchronous and indeterminate divisions that can be modulated by environmental cues. The products of the lineage, stomatal guard cells and pavement cells, regulate plant-atmosphere exchanges, and the epidermis as a whole influences overall leaf growth. How flexibility is encoded in development of the stomatal lineage and how cell fates are coordinated in the leaf are open questions. Here, by leveraging single-cell transcriptomics and molecular genetics, we uncovered models of cell differentiation within Arabidopsis leaf tissue. Profiles across leaf tissues identified points of regulatory congruence. In the stomatal lineage, single-cell resolution resolved underlying cell heterogeneity within early stages and provided a fine-grained profile of guard cell differentiation. Through integration of genome-scale datasets and spatiotemporally precise functional manipulations, we also identified an extended role for the transcriptional regulator SPEECHLESS in reinforcing cell fate commitment.
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Affiliation(s)
- Camila B Lopez-Anido
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Anne Vatén
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Nicole K Smoot
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Nidhi Sharma
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Victoria Guo
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Yan Gong
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - M Ximena Anleu Gil
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Annika K Weimer
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA.
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42
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Mizuno Y, Komatsu A, Shimazaki S, Naramoto S, Inoue K, Xie X, Ishizaki K, Kohchi T, Kyozuka J. Major components of the KARRIKIN INSENSITIVE2-dependent signaling pathway are conserved in the liverwort Marchantia polymorpha. THE PLANT CELL 2021; 33:2395-2411. [PMID: 33839776 PMCID: PMC8364241 DOI: 10.1093/plcell/koab106] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
KARRIKIN INSENSITIVE2 (KAI2) was first identified as a receptor of karrikins, smoke-derived germination stimulants. KAI2 is also considered a receptor of an unidentified endogenous molecule called the KAI2 ligand. Upon KAI2 activation, signals are transmitted through the degradation of D53/SMXL proteins via MAX2-dependent ubiquitination. Although components in the KAI2-dependent signaling pathway, namely MpKAI2A and MpKAI2B, MpMAX2, and MpSMXL, exist in the genome of the liverwort Marchantia polymorpha, their functions remain unknown. Here, we show that early thallus growth is retarded and gemma dormancy in the dark is suppressed in Mpkai2a and Mpmax2 loss-of-function mutants. These defects are counteracted in Mpkai2a Mpsmxl and Mpmax2 Mpsmxl double mutants indicating that MpKAI2A, MpMAX2, and MpSMXL act in the same genetic pathway. Introduction of MpSMXLd53, in which a domain required for degradation is mutated, into wild-type plants mimicks Mpkai2a and Mpmax2 plants. In addition, the detection of citrine fluorescence in Nicotiana benthamiana cells transiently expressing a SMXL-Citrine fusion protein requires treatment with MG132, a proteasome inhibitor. These findings imply that MpSMXL is subjected to degradation, and that the degradation of MpSMXL is crucial for MpKAI2A-dependent signaling in M. polymorpha. Therefore, we claim that the basic mechanisms in the KAI2-dependent signaling pathway are conserved in M. polymorpha.
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Affiliation(s)
- Yohei Mizuno
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Aino Komatsu
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Shota Shimazaki
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Satoshi Naramoto
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Xiaonan Xie
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi 321-8505, Japan
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
- Author for correspondence:
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43
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Marand AP, Chen Z, Gallavotti A, Schmitz RJ. A cis-regulatory atlas in maize at single-cell resolution. Cell 2021; 184:3041-3055.e21. [PMID: 33964211 DOI: 10.1101/2020.09.27.315499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 05/22/2023]
Abstract
cis-regulatory elements (CREs) encode the genomic blueprints of spatiotemporal gene expression programs enabling highly specialized cell functions. Using single-cell genomics in six maize organs, we determined the cis- and trans-regulatory factors defining diverse cell identities and coordinating chromatin organization by profiling transcription factor (TF) combinatorics, identifying TFs with non-cell-autonomous activity, and uncovering TFs underlying higher-order chromatin interactions. Cell-type-specific CREs were enriched for enhancer activity and within unmethylated long terminal repeat retrotransposons. Moreover, we found cell-type-specific CREs are hotspots for phenotype-associated genetic variants and were targeted by selection during modern maize breeding, highlighting the biological implications of this CRE atlas. Through comparison of maize and Arabidopsis thaliana developmental trajectories, we identified TFs and CREs with conserved and divergent chromatin dynamics, showcasing extensive evolution of gene regulatory networks. In addition to this rich dataset, we developed single-cell analysis software, Socrates, which can be used to understand cis-regulatory variation in any species.
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Affiliation(s)
| | - Zongliang Chen
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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A cis-regulatory atlas in maize at single-cell resolution. Cell 2021; 184:3041-3055.e21. [PMID: 33964211 DOI: 10.1016/j.cell.2021.04.014] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
Abstract
cis-regulatory elements (CREs) encode the genomic blueprints of spatiotemporal gene expression programs enabling highly specialized cell functions. Using single-cell genomics in six maize organs, we determined the cis- and trans-regulatory factors defining diverse cell identities and coordinating chromatin organization by profiling transcription factor (TF) combinatorics, identifying TFs with non-cell-autonomous activity, and uncovering TFs underlying higher-order chromatin interactions. Cell-type-specific CREs were enriched for enhancer activity and within unmethylated long terminal repeat retrotransposons. Moreover, we found cell-type-specific CREs are hotspots for phenotype-associated genetic variants and were targeted by selection during modern maize breeding, highlighting the biological implications of this CRE atlas. Through comparison of maize and Arabidopsis thaliana developmental trajectories, we identified TFs and CREs with conserved and divergent chromatin dynamics, showcasing extensive evolution of gene regulatory networks. In addition to this rich dataset, we developed single-cell analysis software, Socrates, which can be used to understand cis-regulatory variation in any species.
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Shi D, Jouannet V, Agustí J, Kaul V, Levitsky V, Sanchez P, Mironova VV, Greb T. Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. THE PLANT CELL 2021; 33:200-223. [PMID: 33582756 PMCID: PMC8136906 DOI: 10.1093/plcell/koaa019] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 05/06/2023]
Abstract
Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next-generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.
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Affiliation(s)
- Dongbo Shi
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Japan Science and Technology Agency (JST), Saitama, Kawaguchi, Japan
| | - Virginie Jouannet
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Javier Agustí
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), C/Enginyer Fausto Elio S/N. 46011 Valencia, Spain
| | - Verena Kaul
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Victor Levitsky
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Pablo Sanchez
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Victoria V Mironova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas Greb
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Author for correspondence:
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Lopez-Anido CB, Vatén A, Smoot NK, Sharma N, Guo V, Gong Y, Anleu Gil MX, Weimer AK, Bergmann DC. Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. Dev Cell 2021; 56:1043-1055.e4. [PMID: 33823130 DOI: 10.1101/2020.09.08.288498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 05/22/2023]
Abstract
Dynamic cell identities underlie flexible developmental programs. The stomatal lineage in the Arabidopsis leaf epidermis features asynchronous and indeterminate divisions that can be modulated by environmental cues. The products of the lineage, stomatal guard cells and pavement cells, regulate plant-atmosphere exchanges, and the epidermis as a whole influences overall leaf growth. How flexibility is encoded in development of the stomatal lineage and how cell fates are coordinated in the leaf are open questions. Here, by leveraging single-cell transcriptomics and molecular genetics, we uncovered models of cell differentiation within Arabidopsis leaf tissue. Profiles across leaf tissues identified points of regulatory congruence. In the stomatal lineage, single-cell resolution resolved underlying cell heterogeneity within early stages and provided a fine-grained profile of guard cell differentiation. Through integration of genome-scale datasets and spatiotemporally precise functional manipulations, we also identified an extended role for the transcriptional regulator SPEECHLESS in reinforcing cell fate commitment.
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Affiliation(s)
- Camila B Lopez-Anido
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Anne Vatén
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Nicole K Smoot
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Nidhi Sharma
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Victoria Guo
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Yan Gong
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - M Ximena Anleu Gil
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Annika K Weimer
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA.
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47
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Song Y, Yang S, Wang J. In vitro and in vivo activity analysis of poplar CLE dodecapeptides that are most divergent from Arabidopsis counterparts. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110832. [PMID: 33691966 DOI: 10.1016/j.plantsci.2021.110832] [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: 10/12/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Intercellular communication mediated by the plant-specific CLAVATA3/ENDOSPERM SURROUNDING REGION (ESR)-related (CLE) family members is one of the fundamental mechanisms coordinating the development of complex bodies of plants. In this work, we chose 8 out of 38 putative CLE dodecapeptides encoded in the genome of P. trichocarpa based on their lowest sequence similarity with Arabidopsis CLE peptides, and investigated how such sequence variations affect their functional characteristics. In group 1, PtCLE16p faithfully retained the AtCLE1-7p activity, while PtCLE49p reversed the root-enhancing effect to an inhibitory one with two extra amino acid substitutions, which might have disrupted the capacity of PtCLE49p to recognize the corresponding receptors. In group 2, PtCLE9p conferred Arabidopsis with retarded root growth and suppressed phloem differentiation in a negative dominant manner just like AtCLE25G6T did. PtCLE9p enhanced the vegetative growth in both basal and aerial rosettes by regulating the expression of AERIAL ROSETTE 1 (ART1) and FRIGIDA (FRI) as well as the downstream FLOWERING LOCUS C (FLC) genes. In group 3, PtCLE34p and PtCLE5p slightly promoted primary root growth, while PtCLE40p revealed CLV3p-like and TDIF activity in root and hypocotyls, respectively. The remaining PtCLE18p in group 4 dramatically disturbed the expression of WOX5 and promoted the development of root hairs by repressing the expression of GLABRA2 (GL2) gene, which encoded a negative regulator of epidermal cells differentiation towards root hairs. In summary, our data indicated that with significant functional conservation and common signaling machinery existing for CLE families of land plants, unique and diverse activities of CLE peptides have evolved to perform specific functions in different plant species.
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Affiliation(s)
- Yawen Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
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48
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Aquino B, Bradley JM, Lumba S. On the outside looking in: roles of endogenous and exogenous strigolactones. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:322-334. [PMID: 33215770 DOI: 10.1111/tpj.15087] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/27/2020] [Accepted: 10/21/2020] [Indexed: 05/15/2023]
Abstract
A collection of small molecules called strigolactones (SLs) act as both endogenous hormones to control plant development and as ecological communication cues between organisms. SL signalling overlaps with that of a class of smoke-derived compounds, karrikins (KARs), which have distinct yet overlapping developmental effects on plants. Although the roles of SLs in shoot and root development, in the promotion of arbuscular mycorrhizal (AM) fungal branching and in parasitic plant germination have been well characterized, recent data have illustrated broader roles for these compounds in the rhizosphere. Here, we review the known roles of SLs in development, growth of AM fungi and germination of parasitic plants to develop a framework for understanding the use of SLs as molecules of communication in the rhizosphere. It appears, for example, that there are many connections between SLs and phosphate utilization. Low phosphate levels regulate SL metabolism and, in turn, SLs sculpt root and shoot architecture to coordinate growth and optimize phosphate uptake from the environment. Plant-exuded SLs attract fungal symbionts to deliver inorganic phosphate (Pi) to the host. These and other examples suggest the boundary between exogenous and endogenous SL functions can be easily blurred and a more holistic view of these small molecules is likely to be required to fully understand SL biology. Related to this, we summarize and discuss evidence for a primitive role of SLs in moss as a quorum sensing-like molecule, providing a unifying concept of SLs as endogenous and exogenous signalling molecules.
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Affiliation(s)
- Bruno Aquino
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, M5S 3B2, Canada
| | - James M Bradley
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, M5S 3B2, Canada
| | - Shelley Lumba
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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Seo M, Kim H, Lee JY. Information on the move: vascular tissue development in space and time during postembryonic root growth. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:110-117. [PMID: 32905917 DOI: 10.1016/j.pbi.2020.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/08/2020] [Accepted: 08/04/2020] [Indexed: 05/27/2023]
Abstract
Cascades of temporal and spatial regulation of gene expression play crucial roles in the vascular development in plant roots. Once vascular cell fates are determined, the timing of their differentiation is tightly controlled in a cell-autonomous manner. In contrast, extensive cell-to-cell communication contributes to the positioning and specifying of vascular cell types in the root meristem. Diverse factors moving short distances in a radial direction were found to be key contributors to these processes. Furthermore, signals from differentiated phloem were found to influence the phloem precursor and determine how the corresponding asymmetric cell division proceeded. These findings highlight the potential importance of underexplored types of intercellular communication in relation to vascular tissue development during postembryonic root growth.
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Affiliation(s)
- Minji Seo
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoujin Kim
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea.
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50
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Agustí J, Blázquez MA. Plant vascular development: mechanisms and environmental regulation. Cell Mol Life Sci 2020; 77:3711-3728. [PMID: 32193607 PMCID: PMC11105054 DOI: 10.1007/s00018-020-03496-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
Abstract
Plant vascular development is a complex process culminating in the generation of xylem and phloem, the plant transporting conduits. Xylem and phloem arise from specialized stem cells collectively termed (pro)cambium. Once developed, xylem transports mainly water and mineral nutrients and phloem transports photoassimilates and signaling molecules. In the past few years, major advances have been made to characterize the molecular, genetic and physiological aspects that govern vascular development. However, less is known about how the environment re-shapes the process, which molecular mechanisms link environmental inputs with developmental outputs, which gene regulatory networks facilitate the genetic adaptation of vascular development to environmental niches, or how the first vascular cells appeared as an evolutionary innovation. In this review, we (1) summarize the current knowledge of the mechanisms involved in vascular development, focusing on the model species Arabidopsis thaliana, (2) describe the anatomical effect of specific environmental factors on the process, (3) speculate about the main entry points through which the molecular mechanisms controlling of the process might be altered by specific environmental factors, and (4) discuss future research which could identify the genetic factors underlying phenotypic plasticity of vascular development.
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Affiliation(s)
- Javier Agustí
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022, Valencia, Spain.
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