51
|
Laohavisit A. Wound-Induced Rooting in Plants-A big BIG ROle Emerges for Calcium and Auxin. PLANT & CELL PHYSIOLOGY 2023; 64:149-151. [PMID: 36688580 DOI: 10.1093/pcp/pcad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Anuphon Laohavisit
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| |
Collapse
|
52
|
Zhai N, Pan X, Zeng M, Xu L. Developmental trajectory of pluripotent stem cell establishment in Arabidopsis callus guided by a quiescent center-related gene network. Development 2023; 150:286991. [PMID: 36762604 DOI: 10.1242/dev.200879] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
In plant tissue culture, callus formation is induced by a high auxin concentration. Among the three cell layers (the outer, middle and inner cell layers) of the callus, pluripotency acquisition in the middle cell layer is required for the potential ability of the callus to regenerate organs. Here, we reveal the developmental trajectory of middle cell layer initiation and maintenance in callus tissue originating from Arabidopsis thaliana hypocotyls. The S phase of the cell cycle is essential for the expression of quiescent center-related SCARECROW (SCR), PLETHORA1 (PLT1) and WUSCHEL-RELATED HOMEOBOX5 (WOX5) genes during the division of callus founder cells to initiate the callus primordium. After callus initiation, SHOOT-ROOT (SHR) proteins move from the inner to the middle cell layer and act together with SCR to promote the expression of PLT1 and WOX5. WOX5 represses the expression of VASCULAR-RELATED NAC-DOMAIN (VND) genes, thereby preventing callus tissue from differentiating into xylem cells. PLT1 and PLT2 directly activate JACKDAW (JKD), which is necessary for pluripotency acquisition in the middle cell layer. We hypothesize that the middle cell layer could have pluripotent stem cell activity and its establishment requires the quiescent center-related SCR-SHR-WOX5-PLT1/2-JKD gene network.
Collapse
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, 300 Fenglin Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xuan Pan
- 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, 300 Fenglin Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Minhuan Zeng
- 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, 300 Fenglin Road, Shanghai 200032, 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, 300 Fenglin Road, Shanghai 200032, China
| |
Collapse
|
53
|
Liu X, Zhu K, Xiao J. Recent advances in understanding of the epigenetic regulation of plant regeneration. ABIOTECH 2023; 4:31-46. [PMID: 37220541 PMCID: PMC10199984 DOI: 10.1007/s42994-022-00093-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/27/2022] [Indexed: 05/22/2023]
Abstract
Ever since the concept of "plant cell totipotency" was first proposed in the early twentieth century, plant regeneration has been a major focus of study. Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture. Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration. The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation. Here, we summarize how various aspects of epigenetic regulation, including histone modifications and variants, chromatin accessibility dynamics, DNA methylation, and microRNAs, modulate plant regeneration. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in boosting crop breeding, especially if coupled with emerging single-cell omics technologies.
Collapse
Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| |
Collapse
|
54
|
Tran S, Ison M, Ferreira Dias NC, Ortega MA, Chen YFS, Peper A, Hu L, Xu D, Mozaffari K, Severns PM, Yao Y, Tsai CJ, Teixeira PJPL, Yang L. Endogenous salicylic acid suppresses de novo root regeneration from leaf explants. PLoS Genet 2023; 19:e1010636. [PMID: 36857386 PMCID: PMC10010561 DOI: 10.1371/journal.pgen.1010636] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 03/13/2023] [Accepted: 01/25/2023] [Indexed: 03/02/2023] Open
Abstract
Plants can regenerate new organs from damaged or detached tissues. In the process of de novo root regeneration (DNRR), adventitious roots are frequently formed from the wound site on a detached leaf. Salicylic acid (SA) is a key phytohormone regulating plant defenses and stress responses. The role of SA and its acting mechanisms during de novo organogenesis is still unclear. Here, we found that endogenous SA inhibited the adventitious root formation after cutting. Free SA rapidly accumulated at the wound site, which was accompanied by an activation of SA response. SA receptors NPR3 and NPR4, but not NPR1, were required for DNRR. Wounding-elevated SA compromised the expression of AUX1, and subsequent transport of auxin to the wound site. A mutation in AUX1 abolished the enhanced DNRR in low SA mutants. Our work elucidates a role of SA in regulating DNRR and suggests a potential link between biotic stress and tissue regeneration.
Collapse
Affiliation(s)
- Sorrel Tran
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Madalene Ison
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | | | - Maria Andrea Ortega
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, Georgia, United States of America
- Department of Plant Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Yun-Fan Stephanie Chen
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Alan Peper
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Lanxi Hu
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Dawei Xu
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Khadijeh Mozaffari
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Paul M. Severns
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Yao Yao
- Department of Animal and Diary Sciences, College of Agricultural & Environmental Sciences, University of Georgia, Georgia, United States of America
| | - Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, Georgia, United States of America
- Department of Plant Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Sao Paulo, Brazil
- * E-mail: (PJPLT); (LY)
| | - Li Yang
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (PJPLT); (LY)
| |
Collapse
|
55
|
Zhang X, Lai C, Xu L, Guan Q, Zhang S, Chen Y, Zhang Z, Chen Y, Lai Z, Lin Y. Integrated proteome and acetylome analyses provide novel insights into early somatic embryogenesis of Dimocarpus longan. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:903-916. [PMID: 36878164 DOI: 10.1016/j.plaphy.2023.02.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Longan (Dimocarpus longan) is a precious subtropical fruit with high nutritional value. The somatic embryogenesis (SE) affects the quality and yield of fruit. Apart from clonal propagation, SE has extensive applications in genetic improvement and mutation. Thus, understanding the molecular basis of embryogenesis in longan will help to develop strategies for mass production of quality planting material. Lysine acetylation (Kac) plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in plant early SE. In this study, the proteome and acetylome of longan embryogenic callus (ECs) and globular embryos (GEs) were investigated. In total, 7232 proteins and 14,597 Kac sites were identified, and this resulted in the discovery of 1178 differentially expressed proteins and 669 differentially expressed acetylated proteins. KEGG and GO analysis showed that glucose metabolism, carbon metabolism, fatty acid degradation, and oxidative phosphorylation pathways were influenced by Kac modification. Furthermore, sodium butyrate (Sb, a deacetylase inhibitor) led to reduced the proliferation and delayed the differentiation of ECs by regulating the homeostasis of reactive oxygen species (ROS) andindole-3-acetic acid (IAA). Our study provides a comprehensive proteomic and acetylomic analysis to aid in understanding the molecular mechanisms involved in early SE, representing a potential tool for genetic improvement of longan.
Collapse
Affiliation(s)
- Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Luzhen Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing Guan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
56
|
Jiang K, Guo H, Zhai J. Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:381-398. [PMID: 36223083 DOI: 10.1111/jipb.13384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.
Collapse
Affiliation(s)
- Kai Jiang
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| |
Collapse
|
57
|
Lee K, Wang K. Strategies for genotype-flexible plant transformation. Curr Opin Biotechnol 2023; 79:102848. [PMID: 36463838 DOI: 10.1016/j.copbio.2022.102848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022]
Abstract
Recent advances in the genome-editing tools have demonstrated a great potential for accelerating functional genomics and crop trait improvements, but the low efficiency and genotype dependence in plant transformation hinder practical applications of such revolutionary tools. Morphogenic transcription factors (MTFs) such as Baby boom, Wuschel2, GROWTH-REGULATING FACTOR5, GROWTH-REGULATING FACTOR4 and its cofactor GRF-INTERACTING FACTOR1, and Wuschel-homeobox 5 related have been shown to greatly enhance plant transformation efficiency and expand the range of amenable species and genotypes. This review will summarize recent advancements in plant transformation technologies with an emphasis on the strategies developed for genotype-flexible transformation methods utilizing MTFs for both monocots and dicot plant species. We highlight several breakthrough studies that demonstrated a wide range of applicability.
Collapse
Affiliation(s)
- Keunsub Lee
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
58
|
Rennolds CW, Bely AE. Integrative biology of injury in animals. Biol Rev Camb Philos Soc 2023; 98:34-62. [PMID: 36176189 PMCID: PMC10087827 DOI: 10.1111/brv.12894] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 01/12/2023]
Abstract
Mechanical injury is a prevalent challenge in the lives of animals with myriad potential consequences for organisms, including reduced fitness and death. Research on animal injury has focused on many aspects, including the frequency and severity of wounding in wild populations, the short- and long-term consequences of injury at different biological scales, and the variation in the response to injury within or among individuals, species, ontogenies, and environmental contexts. However, relevant research is scattered across diverse biological subdisciplines, and the study of the effects of injury has lacked synthesis and coherence. Furthermore, the depth of knowledge across injury biology is highly uneven in terms of scope and taxonomic coverage: much injury research is biomedical in focus, using mammalian model systems and investigating cellular and molecular processes, while research at organismal and higher scales, research that is explicitly comparative, and research on invertebrate and non-mammalian vertebrate species is less common and often less well integrated into the core body of knowledge about injury. The current state of injury research presents an opportunity to unify conceptually work focusing on a range of relevant questions, to synthesize progress to date, and to identify fruitful avenues for future research. The central aim of this review is to synthesize research concerning the broad range of effects of mechanical injury in animals. We organize reviewed work by four broad and loosely defined levels of biological organization: molecular and cellular effects, physiological and organismal effects, behavioural effects, and ecological and evolutionary effects of injury. Throughout, we highlight the diversity of injury consequences within and among taxonomic groups while emphasizing the gaps in taxonomic coverage, causal understanding, and biological endpoints considered. We additionally discuss the importance of integrating knowledge within and across biological levels, including how initial, localized responses to injury can lead to long-term consequences at the scale of the individual animal and beyond. We also suggest important avenues for future injury biology research, including distinguishing better between related yet distinct injury phenomena, expanding the subjects of injury research to include a greater variety of species, and testing how intrinsic and extrinsic conditions affect the scope and sensitivity of injury responses. It is our hope that this review will not only strengthen understanding of animal injury but will contribute to building a foundation for a more cohesive field of 'injury biology'.
Collapse
Affiliation(s)
- Corey W Rennolds
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Alexandra E Bely
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| |
Collapse
|
59
|
Liang Y, Heyman J, Lu R, De Veylder L. Evolution of wound-activated regeneration pathways in the plant kingdom. Eur J Cell Biol 2023; 102:151291. [PMID: 36709604 DOI: 10.1016/j.ejcb.2023.151291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Regeneration serves as a self-protective mechanism that allows a tissue or organ to recover its entire form and function after suffering damage. However, the regenerative capacity varies greatly within the plant kingdom. Primitive plants frequently display an amazing regenerative ability as they have developed a complex system and strategy for long-term survival under extreme stress conditions. The regenerative ability of dicot species is highly variable, but that of monocots often exhibits extreme recalcitrance to tissue replenishment. Recent studies have revealed key factors and signals that affect cell fate during plant regeneration, some of which are conserved among the plant lineage. Among these, several members of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors have been implicated in wound signaling, playing crucial roles in the regenerative mechanisms after different types of wounding. An understanding of plant regeneration may ultimately lead to an increased regenerative potential of recalcitrant species, producing more high-yielding, multi-resistant and environmentally friendly crops and ensuring the long-term development of global agriculture.
Collapse
Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
| |
Collapse
|
60
|
Wan Q, Zhai N, Xie D, Liu W, Xu L. WOX11: the founder of plant organ regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:1. [PMID: 36596978 PMCID: PMC9810776 DOI: 10.1186/s13619-022-00140-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023]
Abstract
De novo organ regeneration is the process in which adventitious roots or shoots regenerate from detached or wounded organs. De novo organ regeneration can occur either in natural conditions, e.g. adventitious root regeneration from the wounded sites of detached leaves or stems, or in in-vitro tissue culture, e.g. organ regeneration from callus. In this review, we summarize recent advances in research on the molecular mechanism of de novo organ regeneration, focusing on the role of the WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene in the model plant Arabidopsis thaliana. WOX11 is a direct target of the auxin signaling pathway, and it is expressed in, and regulates the establishment of, the founder cell during de novo root regeneration and callus formation. WOX11 activates the expression of its target genes to initiate root and callus primordia. Therefore, WOX11 links upstream auxin signaling to downstream cell fate transition during regeneration. We also discuss the role of WOX11 in diverse species and its evolution in plants.
Collapse
Affiliation(s)
- Qihui Wan
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049 China
| | - Ning Zhai
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China
| | - Dixiang Xie
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049 China
| | - Wu Liu
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China
| | - Lin Xu
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China
| |
Collapse
|
61
|
Cao Y, Koh SS, Han Y, Tan JJ, Kim D, Chua NH, Urano D, Marelli B. Drug Delivery in Plants Using Silk Microneedles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2205794. [PMID: 36245320 DOI: 10.1002/adma.202205794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/04/2022] [Indexed: 06/16/2023]
Abstract
New systems for agrochemical delivery in plants will foster precise agricultural practices and provide new tools to study plants and design crop traits, as standard spray methods suffer from elevated loss and limited access to remote plant tissues. Silk-based microneedles can circumvent these limitations by deploying a known amount of payloads directly in plants' deep tissues. However, plant response to microneedles' application and microneedles' efficacy in deploying physiologically relevant biomolecules are unknown. Here, it is shown that gene expression associated with Arabidopsis thaliana wounding response decreases within 24 h post microneedles' application. Additionally, microinjection of gibberellic acid (GA3 ) in A. thaliana mutant ft-10 provides a more effective and efficient mean than spray to activate GA3 pathways, accelerating bolting and inhibiting flower formation. Microneedle efficacy in delivering GA3 is also observed in several monocot and dicot crop species, i.e., tomato (Solanum lycopersicum), lettuce (Lactuca sativa), spinach (Spinacia oleracea), rice (Oryza Sativa), maize (Zea mays), barley (Hordeum vulgare), and soybean (Glycine max). The wide range of plants that can be successfully targeted with microinjectors opens the doors to their use in plant science and agriculture.
Collapse
Affiliation(s)
- Yunteng Cao
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sally Shuxian Koh
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 119077, Singapore
| | - Yangyang Han
- Singapore-MIT Alliance for Research and Technology, Singapore, 119077, Singapore
| | - Javier Jingheng Tan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
| | - Doyoon Kim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Singapore-MIT Alliance for Research and Technology, Singapore, 119077, Singapore
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 119077, Singapore
- Singapore-MIT Alliance for Research and Technology, Singapore, 119077, Singapore
| | - Benedetto Marelli
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Singapore-MIT Alliance for Research and Technology, Singapore, 119077, Singapore
| |
Collapse
|
62
|
Wu G, Wei X, Wang X, Wei Y. Changes and transcriptome regulation of endogenous hormones during somatic embryogenesis in Ormosia henryi Prain. FRONTIERS IN PLANT SCIENCE 2023; 14:1121259. [PMID: 37077643 PMCID: PMC10106752 DOI: 10.3389/fpls.2023.1121259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
Introduction Ormosia henryi is a rare and endangered plant growing in southern China. Somatic embryo culture is an effective measure for the rapid propagation of O. henryi. It has not been reported how regulatory genes induce somatic embryogenesis by regulating endogenous hormone changes during the process of somatic embryogenesis in O. henryi. Methods In this study, we analysed the endogenous hormone levels and transcriptome data of nonembryogenic callus (NEC), embryogenic callus (EC), globular embryo (GE) and cotyledon embryo (CE) in O. henryi. Results The results showed that the indole-3-acetic acid (IAA) content was higher and the cytokinins (CKs) content was lower in EC than in NEC, and the gibberellins (GAs) and abscisic acid (ABA) contents were significantly higher in NEC than in EC. The contents of IAA, CKs, GAs and ABA increased significantly with EC development. The expression patterns of differentially expressed genes (DEGs) involved in the biosynthesis and signal transduction of auxin (AUX) (YUCCA and SAUR), CKs (B-ARR), GAs (GA3ox, GA20ox, GID1 and DELLA) and ABA (ZEP, ABA2, AAO3, CYP97A3, PYL and ABF) were consistent with the levels of endogenous hormones during somatic embryogenesis (SE). In this study, 316 different transcription factors (TFs) regulating phytohormones were detected during SE. AUX/IAA were downregulated in the process of EC formation and GE differentiation into CE, but other TFs were upregulated and downregulated. Conclusion Therefore, we believe that relatively high IAA content and low CKs, GAs and ABA contents contribute to EC formation. The differential expression of AUX, CKs, GAs and ABA biosynthesis and signal transduction genes affected the endogenous hormone levels at different stages of SE in O. henryi. The downregulated expression of AUX/IAA inhibited NEC induction, promoted EC formation and GE differentiation into CE.
Collapse
Affiliation(s)
- Gaoyin Wu
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
- College of Life Science, Guizhou Normal University, Guiyang, Guizhou, China
- *Correspondence: Wei Xiaoli, ; Wu Gaoyin,
| | - Xiaoli Wei
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
- *Correspondence: Wei Xiaoli, ; Wu Gaoyin,
| | - Xiao Wang
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
| | - Yi Wei
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
| |
Collapse
|
63
|
Omary M, Matosevich R, Efroni I. Systemic control of plant regeneration and wound repair. THE NEW PHYTOLOGIST 2023; 237:408-413. [PMID: 36101501 PMCID: PMC10092612 DOI: 10.1111/nph.18487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Plants have a broad capacity to regenerate damaged organs. The study of wounding in multiple developmental systems has uncovered many of the molecular properties underlying plants' competence for regeneration at the local cellular level. However, in nature, wounding is rarely localized to one place, and plants need to coordinate regeneration responses at multiple tissues with environmental conditions and their physiological state. Here, we review the evidence for systemic signals that regulate regeneration on a plant-wide level. We focus on the role of auxin and sugars as short- and long-range signals in natural wounding contexts and discuss the varied origin of these signals in different regeneration scenarios. Together, this evidence calls for a broader, system-wide view of plant regeneration competence.
Collapse
Affiliation(s)
- Moutasem Omary
- The Institute of Plant Sciences, Faculty of AgricultureThe Hebrew UniversityRehovot761000Israel
| | - Rotem Matosevich
- The Institute of Plant Sciences, Faculty of AgricultureThe Hebrew UniversityRehovot761000Israel
| | - Idan Efroni
- The Institute of Plant Sciences, Faculty of AgricultureThe Hebrew UniversityRehovot761000Israel
| |
Collapse
|
64
|
Larriba E, Nicolás-Albujer M, Sánchez-García AB, Pérez-Pérez JM. Identification of Transcriptional Networks Involved in De Novo Organ Formation in Tomato Hypocotyl Explants. Int J Mol Sci 2022; 23:ijms232416112. [PMID: 36555756 PMCID: PMC9788163 DOI: 10.3390/ijms232416112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
Collapse
|
65
|
Nuzzo F, Gambino G, Perrone I. Unlocking grapevine in vitro regeneration: Issues and perspectives for genetic improvement and functional genomic studies. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:99-109. [PMID: 36343465 DOI: 10.1016/j.plaphy.2022.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
In vitro plant regeneration is a pivotal process in genetic engineering to obtain large numbers of transgenic, cisgenic and gene edited plants in the frame of functional gene or genetic improvement studies. However, several issues emerge as regeneration is not universally possible across the plant kingdom and many variables must be considered. In grapevine (Vitis spp.), as in other woody and fruit tree species, the regeneration process is impaired by a recalcitrance that depends on numerous factors such as genotype and explant-dependent responses. This is one of the major obstacles in developing gene editing approaches and functional genome studies in grapevine and it is therefore crucial to understand how to achieve efficient regeneration across different genotypes. Further issues that emerge in regeneration need to be addressed, such as somaclonal mutations which do not allow the regeneration of individuals identical to the original mother plant, an essential factor for commercial use of the improved grapevines obtained through the New Breeding Techniques. Over the years, the evolution of protocols to achieve plant regeneration has relied mainly on optimizing protocols for genotypes of interest whilst nowadays with new genomic data available there is an emerging opportunity to have a clearer picture of its molecular regulation. The goal of this review is to discuss the latest information available about different aspects of grapevine in vitro regeneration, to address the main factors that can impair the efficiency of the plant regeneration process and cause post-regeneration problems and to propose strategies for investigating and solving them.
Collapse
Affiliation(s)
- Floriana Nuzzo
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy.
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
| |
Collapse
|
66
|
Shin SY, Choi Y, Kim SG, Park SJ, Park JS, Moon KB, Kim HS, Jeon JH, Cho HS, Lee HJ. Submergence promotes auxin-induced callus formation through ethylene-mediated post-transcriptional control of auxin receptors. MOLECULAR PLANT 2022; 15:1947-1961. [PMID: 36333910 DOI: 10.1016/j.molp.2022.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Plant cells in damaged tissue can be reprogrammed to acquire pluripotency and induce callus formation. However, in the aboveground organs of many species, somatic cells that are distal to the wound site become less sensitive to auxin-induced callus formation, suggesting the existence of repressive regulatory mechanisms that are largely unknown. Here we reveal that submergence-induced ethylene signals promote callus formation by releasing post-transcriptional silencing of auxin receptor transcripts in non-wounded regions. We determined that short-term submergence of intact seedlings induces auxin-mediated cell dedifferentiation across the entirety of Arabidopsis thaliana explants. The constitutive triple response 1-1 (ctr1-1) mutation induced callus formation in explants without submergence, suggesting that ethylene facilitates cell dedifferentiation. We show that ETHYLENE-INSENSITIVE 2 (EIN2) post-transcriptionally regulates the abundance of transcripts for auxin receptor genes by facilitating microRNA393 degradation. Submergence-induced calli in non-wounded regions were suitable for shoot regeneration, similar to those near the wound site. We also observed submergence-promoted callus formation in Chinese cabbage (Brassica rapa), indicating that this may be a conserved mechanism in other species. Our study identifies previously unknown regulatory mechanisms by which ethylene promotes cell dedifferentiation and provides a new approach for boosting callus induction efficiency in shoot explants.
Collapse
Affiliation(s)
- Seung Yong Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Yuri Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
| | - Jae Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea.
| |
Collapse
|
67
|
Ma J, Li Q, Zhang L, Cai S, Liu Y, Lin J, Huang R, Yu Y, Wen M, Xu T. High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2425-2437. [PMID: 36250442 DOI: 10.1111/jipb.13387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Callus induction, which results in fate transition in plant cells, is considered as the first and key step for plant regeneration. This process can be stimulated in different tissues by a callus-inducing medium (CIM), which contains a high concentration of phytohormone auxin. Although a few key regulators for callus induction have been identified, the multiple aspects of the regulatory mechanism driven by high levels of auxin still need further investigation. Here, we find that high auxin induces callus through a H3K36 histone methylation-dependent mechanism, which requires the methyltransferase SET DOMAIN GROUP 8 (SDG8). During callus induction, the increased auxin accumulates SDG8 expression through a TIR1/AFBs-based transcriptional regulation. SDG8 then deposits H3K36me3 modifications on the loci of callus-related genes, including a master regulator WOX5 and the cell proliferation-related genes, such as CYCB1.1. This epigenetic regulation in turn is required for the transcriptional activation of these genes during callus formation. These findings suggest that the massive transcriptional reprogramming for cell fate transition by auxin during callus formation requires epigenetic modifications including SDG8-mediated histone H3K36 methylation. Our results provide insight into the coordination between auxin signaling and epigenetic regulation during fundamental processes in plant development.
Collapse
Affiliation(s)
- Jun Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiang Li
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Lei Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sen Cai
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Liu
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Juncheng Lin
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rongfeng Huang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongqiang Yu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingzhang Wen
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Tongda Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| |
Collapse
|
68
|
Chen Z, Debernardi JM, Dubcovsky J, Gallavotti A. Recent advances in crop transformation technologies. NATURE PLANTS 2022; 8:1343-1351. [PMID: 36522447 DOI: 10.1038/s41477-022-01295-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/30/2022] [Indexed: 05/12/2023]
Abstract
Agriculture is experiencing a technological inflection point in its history, while also facing unprecedented challenges posed by human population growth and global climate changes. Key advancements in precise genome editing and new methods for rapid generation of bioengineered crops promise to both revolutionize the speed and breadth of breeding programmes and increase our ability to feed and sustain human population growth. Although genome editing enables targeted and specific modifications of DNA sequences, several existing barriers prevent the widespread adoption of editing technologies for basic and applied research in established and emerging crop species. Inefficient methods for the transformation and regeneration of recalcitrant species and the genotype dependency of the transformation process remain major hurdles. These limitations are frequent in monocotyledonous crops, which alone provide most of the calories consumed by human populations. Somatic embryogenesis and de novo induction of meristems - pluripotent groups of stem cells responsible for plant developmental plasticity - are essential strategies to quickly generate transformed plants. Here we review recent discoveries that are rapidly advancing nuclear transformation technologies and promise to overcome the obstacles that have so far impeded the widespread adoption of genome editing in crop species.
Collapse
Affiliation(s)
- Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | - Juan M Debernardi
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA.
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA.
| |
Collapse
|
69
|
Wang FX, Shang GD, Wang JW. Towards a hierarchical gene regulatory network underlying somatic embryogenesis. TRENDS IN PLANT SCIENCE 2022; 27:1209-1217. [PMID: 35810071 DOI: 10.1016/j.tplants.2022.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Genome-editing technologies have advanced in recent years but designing future crops remains limited by current methods of improving somatic embryogenesis (SE) capacity. In this Opinion, we provide an update on the molecular event by which the phytohormone auxin promotes the acquisition of plant cell totipotency through evoking massive changes in transcriptome and chromatin accessibility. We propose that the chromatin states and individual totipotency-related transcription factors (TFs) from disparate gene families organize into a hierarchical gene regulatory network underlying SE. We conclude with a discussion of the practical paths to probe the cellular origin of the somatic embryo and the epigenetic landscape of the totipotent cell state in the era of single-cell genomics.
Collapse
Affiliation(s)
- Fu-Xiang Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China
| | - Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; University of Chinese Academy of Sciences (UCAS), Shanghai 200032, PR China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; ShanghaiTech University, Shanghai 200031, PR China.
| |
Collapse
|
70
|
Shu H, Zhang Y, He C, Altaf MA, Hao Y, Liao D, Li L, Li C, Fu H, Cheng S, Zhu G, Wang Z. Establishment of in vitro regeneration system and molecular analysis of early development of somatic callus in Capsicum chinense and Capsicum baccatum. FRONTIERS IN PLANT SCIENCE 2022; 13:1025497. [PMID: 36466290 PMCID: PMC9714296 DOI: 10.3389/fpls.2022.1025497] [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: 08/23/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Regeneration is extremely important to pepper genetic development; however, the molecular mechanisms of how the callus reactivates cell proliferation and promotes cell reprogramming remain elusive in pepper. In the present study, C. baccatum (HNUCB81 and HNUCB226) and C. chinense (HNUCC22 and HNUCC16) were analyzed to reveal callus initiation by in vitro regeneration, histology, and transcriptome. We successfully established an efficient in vitro regeneration system of two cultivars to monitor the callus induction of differential genotypes, and the regenerated plants were obtained. Compared to C. chinense, there was a higher callus induction rate in C. baccatum. The phenotype of C. baccatum changed significantly and formed vascular tissue faster than C. chinense. The KEGG enrichment analysis found that plant hormone transduction and starch and sucrose metabolism pathways were significantly enriched. In addition, we identified that the WOX7 gene was significantly up-regulated in HNUCB81 and HNUCB226 than that in HNUCC22 and HNUCC16, which may be a potential function in callus formation. These results provided a promising strategy to improve the regeneration and transformation of pepper plants.
Collapse
Affiliation(s)
- Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yu Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Chengyao He
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Muhammad Ahsan Altaf
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Yuanyuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Daolong Liao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Institute of Vegetables, Hainan Province Academy of Agricultural Sciences, Haikou, China
| | - Lin Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Caichao Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Huizhen Fu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
| | - Guopeng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| |
Collapse
|
71
|
Tzeela P, Yechezkel S, Serero O, Eliyahu A, Sherf S, Manni Y, Doron-Faigenboim A, Carmelli-Weissberg M, Shaya F, Dwivedi V, Sadot E. Comparing adventitious root-formation and graft-unification abilities in clones of Argania spinosa. FRONTIERS IN PLANT SCIENCE 2022; 13:1002703. [PMID: 36452103 PMCID: PMC9702570 DOI: 10.3389/fpls.2022.1002703] [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: 07/25/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Argania spinosa trees have attracted attention in recent years due to their high resistance to extreme climate conditions. Initial domestication activities practiced in Morocco. Here we report on selection and vegetative propagation of A. spinosa trees grown in Israel. Trees yielding relatively high amounts of fruit were propagated by rooting of stem cuttings. High variability in rooting ability was found among the 30 clones selected. In-depth comparison of a difficult-to-root (ARS7) and easy-to-root (ARS1) clone revealed that the rooted cuttings of ARS7 have a lower survival rate than those of ARS1. In addition, histological analysis of the adventitious root primordia showed many abnormal fused primordia in ARS7. Hormone profiling revealed that while ARS1 accumulates more cytokinin, ARS7 accumulates more auxin, suggesting different auxin-to-cytokinin ratios underlying the different rooting capabilities. The hypothesized relationship between rooting and grafting abilities was addressed. Reciprocal grafting was performed with ARS1/ARS7 but no significant differences in the success of graft unification between the trees was detected. Accordingly, comparative RNA sequencing of the rooting and grafting zones showed more differentially expressed genes related to rooting than to grafting between the two trees. Clustering, KEGG and Venn analyses confirmed enrichment of genes related to auxin metabolism, transport and signaling, cytokinin metabolism and signaling, cell wall modification and cell division in both regions. In addition, the differential expression of some key genes in ARS1 vs. ARS7 rooting zones was revealed. Taken together, while both adventitious root-formation and graft-unification processes share response to wounding, cell reprogramming, cell division, cell differentiation and reconnection of the vasculature, there are similar, but also many different genes regulating the two processes. Therefore an individual genotype can have low rooting capacity but good graft-unification ability.
Collapse
Affiliation(s)
- Pann Tzeela
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sela Yechezkel
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| | - Ori Serero
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avi Eliyahu
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sara Sherf
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| | - Yair Manni
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| | - Adi Doron-Faigenboim
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| | - Mira Carmelli-Weissberg
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| | - Felix Shaya
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| | - Vikas Dwivedi
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| | - Einat Sadot
- The Institute of Plant Sciences, Agricultural Research Organization-The Volcani Institute, Rishon LeZion, Israel
| |
Collapse
|
72
|
Cordeiro D, Canhoto J, Correia S. Regulatory non-coding RNAs: Emerging roles during plant cell reprogramming and in vitro regeneration. FRONTIERS IN PLANT SCIENCE 2022; 13:1049631. [PMID: 36438127 PMCID: PMC9684189 DOI: 10.3389/fpls.2022.1049631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Plant regeneration is a well-known capacity of plants occurring either in vivo or in vitro. This potential is the basis for plant micropropagation and genetic transformation as well as a useful system to analyse different aspects of plant development. Recent studies have proven that RNA species with no protein-coding capacity are key regulators of cellular function and essential for cell reprogramming. In this review, the current knowledge on the role of several ncRNAs in plant regeneration processes is summarized, with a focus on cell fate reprogramming. Moreover, the involvement/impact of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and small-interfering RNAs (siRNAs) in the regulatory networks of cell dedifferentiation, proliferation and differentiation is also analysed. A deeper understanding of plant ncRNAs in somatic cell reprogramming will allow a better modulation of in vitro regeneration processes such as organogenesis and somatic embryogenesis.
Collapse
|
73
|
Wu H, Zhang K, Zhang Z, Wang J, Jia P, Cong L, Li J, Duan Y, Ke F, Zhang F, Liu Z, Lu F, Wang Y, Li Z, Chang M, Zou J, Zhu K. Cell-penetrating peptide: A powerful delivery tool for DNA-free crop genome editing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111436. [PMID: 36037982 DOI: 10.1016/j.plantsci.2022.111436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/24/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Genome editing system based on the CRISPR/Cas (clustered regularly interspaced short palindromic repeats) technology is a milestone for biology. However, public concerns regarding genetically modified organisms (GMOs) and recalcitrance in the crop of choice for regeneration have limited its application. Cell-penetrating peptides (CPPs) are derived from protein transduction domains (PTDs) that can take on various cargoes across the plant wall, and membrane of target cells. Selected CPPs show mild cytotoxicity and are a suitable delivery tool for DNA-free genome editing. Moreover, CPPs may also be applied for the transient delivery of morphogenic transcription factors, also known as developmental regulators (DRs), to overcome the bottleneck of the crop of choice regeneration. In this review, we introduce a brief history of cell-penetrating peptides and discuss the practice of CPP-mediated DNA-free transfection and the prospects of this potential delivery tool for improving crop genome editing.
Collapse
Affiliation(s)
- Han Wu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China.
| | - Kuangye Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Zhipeng Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Jiaxu Wang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Pengxiang Jia
- Zhejiang Wanli University, 315100 Ningbo, Zhejiang Province, China
| | - Ling Cong
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Jia Li
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Youhou Duan
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Fulai Ke
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Fei Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Zhiqiang Liu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Feng Lu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Yanqiu Wang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Zhihua Li
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Ming Chang
- The Key Laboratory of Bio-interactions and Plant Health, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jianqiu Zou
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China.
| | - Kai Zhu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China.
| |
Collapse
|
74
|
Sakamoto Y, Kawamura A, Suzuki T, Segami S, Maeshima M, Polyn S, De Veylder L, Sugimoto K. Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells. THE PLANT CELL 2022; 34:4348-4365. [PMID: 35922895 PMCID: PMC9614439 DOI: 10.1093/plcell/koac218] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/19/2022] [Indexed: 05/26/2023]
Abstract
Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. In this study, we demonstrate that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis (Arabidopsis thaliana) leaf cells. Our data show that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts. Histone acetylation permits transcriptional activation of PLETHORAs, leading to the induction of their downstream YUCCA1 gene encoding an enzyme for auxin biosynthesis. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for cell cycle reactivation by transcriptionally upregulating MYB3R4. These findings provide a mechanistic model of how differentiated plant cells revert their fate and reinitiate the cell cycle to become pluripotent.
Collapse
Affiliation(s)
- Yuki Sakamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Ayako Kawamura
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Shoji Segami
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Masayoshi Maeshima
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Stefanie Polyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | | |
Collapse
|
75
|
Deng J, Sun W, Zhang B, Sun S, Xia L, Miao Y, He L, Lindsey K, Yang X, Zhang X. GhTCE1-GhTCEE1 dimers regulate transcriptional reprogramming during wound-induced callus formation in cotton. THE PLANT CELL 2022; 34:4554-4568. [PMID: 35972347 PMCID: PMC9614502 DOI: 10.1093/plcell/koac252] [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: 02/17/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Wounded plant cells can form callus to seal the wound site. Alternatively, wounding can cause adventitious organogenesis or somatic embryogenesis. These distinct developmental pathways require specific cell fate decisions. Here, we identify GhTCE1, a basic helix-loop-helix family transcription factor, and its interacting partners as a central regulatory module of early cell fate transition during in vitro dedifferentiation of cotton (Gossypium hirsutum). RNAi- or CRISPR/Cas9-mediated loss of GhTCE1 function resulted in excessive accumulation of reactive oxygen species (ROS), arrested callus cell elongation, and increased adventitious organogenesis. In contrast, GhTCE1-overexpressing tissues underwent callus cell growth, but organogenesis was repressed. Transcriptome analysis revealed that several pathways depend on proper regulation of GhTCE1 expression, including lipid transfer pathway components, ROS homeostasis, and cell expansion. GhTCE1 bound to the promoters of the target genes GhLTP2 and GhLTP3, activating their expression synergistically, and the heterodimer TCE1-TCEE1 enhances this activity. GhLTP2- and GhLTP3-deficient tissues accumulated ROS and had arrested callus cell elongation, which was restored by ROS scavengers. These results reveal a unique regulatory network involving ROS and lipid transfer proteins, which act as potential ROS scavengers. This network acts as a switch between unorganized callus growth and organized development during in vitro dedifferentiation of cotton cells.
Collapse
Affiliation(s)
| | | | - Boyang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Simin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Linjie Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuhuan Miao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangrong He
- Authors for correspondence: (X.Y.), (L.K.), (L.H.)
| | | | - Xiyan Yang
- Authors for correspondence: (X.Y.), (L.K.), (L.H.)
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
76
|
Temmerman A, Marquez-Garcia B, Depuydt S, Bruznican S, De Cuyper C, De Keyser A, Boyer FD, Vereecke D, Struk S, Goormachtig S. MAX2-dependent competence for callus formation and shoot regeneration from Arabidopsis thaliana root explants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6272-6291. [PMID: 35738874 DOI: 10.1093/jxb/erac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/23/2022] [Indexed: 05/21/2023]
Abstract
Although the division of the pericycle cells initiates both lateral root development and root-derived callus formation, these developmental processes are affected differently in the strigolactone and karrikin/KARRIKIN INSENSITIVE 2 (KAI2) ligand signalling mutant more axillary growth 2 (max2). Whereas max2 produces more lateral roots than the wild type, it is defective in the regeneration of shoots from root explants. We suggest that the decreased shoot regeneration of max2 originates from delayed formation of callus primordium, yielding less callus material to regenerate shoots. Indeed, when incubated on callus-inducing medium, the pericycle cell division was reduced in max2 and the early gene expression varied when compared with the wild type, as determined by a transcriptomics analysis. Furthermore, the expression of the LATERAL ORGAN BOUNDARIES DOMAIN genes and of callus-induction genes was modified in correlation with the max2 phenotype, suggesting a role for MAX2 in the regulation of the interplay between cytokinin, auxin, and light signalling in callus initiation. Additionally, we found that the in vitro shoot regeneration phenotype of max2 might be caused by a defect in KAI2, rather than in DWARF14, signalling. Nevertheless, the shoot regeneration assays revealed that the strigolactone biosynthesis mutants max3 and max4 also play a minor role.
Collapse
Affiliation(s)
- Arne Temmerman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Belen Marquez-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Stephen Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, Yeonsu-Gu, Incheon, Korea
| | - Silvia Bruznican
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Carolien De Cuyper
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - François-Didier Boyer
- Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette, France
| | - Danny Vereecke
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg, Ghent, Belgium
| | - Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| |
Collapse
|
77
|
Aflaki F, Gutzat R, Mozgová I. Chromatin during plant regeneration: Opening towards root identity? CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102265. [PMID: 35988353 DOI: 10.1016/j.pbi.2022.102265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Plants show exceptional developmental plasticity and the ability to reprogram cell identities during regeneration. Although regeneration has been used in plant propagation for decades, we only recently gained detailed cellular and molecular insights into this process. Evidently, not all cell types have the same regeneration potential, and only a subset of regeneration-competent cells reach pluripotency. Pluripotent cells exhibit transcriptional similarity to root stem cells. In different plant regeneration systems, transcriptional reprogramming involves transient release of chromatin repression during pluripotency establishment and its restoration during organ or embryo differentiation. Incomplete resetting of the epigenome leads to somaclonal variation in regenerated plants. As single-cell technologies advance, we expect novel, exciting insights into epigenome dynamics during the establishment of pluripotency.
Collapse
Affiliation(s)
- Fatemeh Aflaki
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, 1030, Austria
| | - Iva Mozgová
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic.
| |
Collapse
|
78
|
Glanc M. Plant cell division from the perspective of polarity. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5361-5371. [PMID: 35604840 DOI: 10.1093/jxb/erac227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The orientation of cell division is a major determinant of plant morphogenesis. In spite of considerable efforts over the past decades, the precise mechanism of division plane selection remains elusive. The majority of studies on the topic have addressed division orientation from either a predominantly developmental or a cell biological perspective. Thus, mechanistic insights into the links between developmental and cellular factors affecting division orientation are particularly lacking. Here, I review recent progress in the understanding of cell division orientation in the embryo and primary root meristem of Arabidopsis from both developmental and cell biological standpoints. I offer a view of multilevel polarity as a central aspect of cell division: on the one hand, the division plane is a readout of tissue- and organism-wide polarities; on the other hand, the cortical division zone can be seen as a transient polar subcellular plasma membrane domain. Finally, I argue that a polarity-focused conceptual framework and the integration of developmental and cell biological approaches hold great promise to unravel the mechanistic basis of plant cell division orientation in the near future.
Collapse
Affiliation(s)
- Matouš Glanc
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| |
Collapse
|
79
|
Lardon R, Trinh HK, Xu X, Vu LD, Van De Cotte B, Pernisová M, Vanneste S, De Smet I, Geelen D. Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants. FRONTIERS IN PLANT SCIENCE 2022; 13:894208. [PMID: 36684719 PMCID: PMC9847488 DOI: 10.3389/fpls.2022.894208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.
Collapse
Affiliation(s)
- Robin Lardon
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hoang Khai Trinh
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Biotechnology Research and Development Institute, Can Tho University, Can Tho, Vietnam
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Markéta Pernisová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Steffen Vanneste
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, South Korea
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| |
Collapse
|
80
|
Kang J, Wang X, Ishida T, Grienenberger E, Zheng Q, Wang J, Zhang Y, Chen W, Chen M, Song XF, Wu C, Hu Z, Jia L, Li C, Liu CM, Fletcher JC, Sawa S, Wang G. A group of CLE peptides regulates de novo shoot regeneration in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 235:2300-2312. [PMID: 35642449 DOI: 10.1111/nph.18291] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Known for their regulatory roles in stem cell homeostasis, CLAVATA3/ESR-RELATED (CLE) peptides also function as mediators of external stimuli such as hormones. De novo shoot regeneration, representing the remarkable plant cellular plasticity, involves reconstitution of stem cells under control of stem-cell regulators. Yet whether and how stem cell-regulating CLE peptides are implicated in plant regeneration remains unknown. By CRISPR/Cas9-induced loss-of-function studies, peptide application, precursor overexpression, and expression analyses, the role of CLE1-CLE7 peptides and their receptors in de novo shoot regeneration was studied in Arabidopsis thaliana. CLE1-CLE7 are induced by callus-induction medium and dynamically expressed in pluripotent callus. Exogenously-applied CLE1-CLE7 peptides or precursor overexpression effectively leads to shoot regeneration suppression, whereas their simultaneous mutation results in enhanced regenerative capacity, demonstrating that CLE1-CLE7 peptides redundantly function as negative regulators of de novo shoot regeneration. CLE1-CLE7-mediated shoot regeneration suppression is impaired in loss-of-function mutants of callus-expressed CLAVATA1 (CLV1) and BARELY ANY MERISTEM1 (BAM1) genes, indicating that CLV1/BAM1 are required for CLE1-CLE7-mediated shoot regeneration signaling. CLE1-CLE7 signaling resulted in transcriptional repression of WUSCHEL (WUS), a stem cell-promoting transcription factor known as a principal regulator of plant regeneration. Our results indicate that functionally-redundant CLE1-CLE7 peptides genetically act through CLV1/BAM1 receptors and repress WUS expression to modulate shoot-regeneration capacity, establishing the mechanistic basis for CLE1-CLE7-mediated shoot regeneration and a novel role for CLE peptides in hormone-dependent developmental plasticity.
Collapse
Affiliation(s)
- Jingke Kang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xuening Wang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Takashi Ishida
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, 860-8555, Japan
| | - Etienne Grienenberger
- Plant Gene Expression Center, USDA-ARS/UC Berkeley, Albany, CA, 94710, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Qian Zheng
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Jing Wang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, Shiyan, 442000, China
| | - Wenqiang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengmeng Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu-Fen Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengyun Wu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhubing Hu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lingyu Jia
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Chen Li
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, Shiyan, 442000, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jennifer C Fletcher
- Plant Gene Expression Center, USDA-ARS/UC Berkeley, Albany, CA, 94710, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Shinichiro Sawa
- International Research Center for Agricultural and Environmental Biology (IRCAEB), 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Guodong Wang
- National Engineering Laboratory for Endangered Medicinal Resource Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| |
Collapse
|
81
|
Fang SC, Chen JC, Chang PY, Lin HY. Co-option of the SHOOT MERISTEMLESS network regulates protocorm-like body development in Phalaenopsis aphrodite. PLANT PHYSIOLOGY 2022; 190:127-145. [PMID: 35258627 PMCID: PMC9434259 DOI: 10.1093/plphys/kiac100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/08/2022] [Indexed: 06/02/2023]
Abstract
The protocorm is a structure that is formed upon germination of an orchid seed. It lacks cotyledons and is ovoid in shape. The protocorm-like body (PLB), on the other hand, is a protocorm-like organ induced from somatic tissues. PLBs have been widely used for orchid micropropagation. Because of its unique structure and its application in the orchid industry, PLB development has drawn considerable interest from orchid and developmental biologists. Our previous genome-wide comparative transcriptome study demonstrated that protocorms and PLBs share similar molecular signatures and suggested that SHOOT MERISTEMLESS (STM)-dependent organogenesis is important for PLB development. Here, we show that overexpression of Phalaenopsis aphrodite STM (PaSTM) greatly enhances PLB regeneration from vegetative tissue-based explants of Phalaenopsis orchids, confirming its regulatory role in PLB development. Expression of PaSTM restored shoot meristem function of the Arabidopsis (Arabidopsis thaliana) stm-2 mutant. Moreover, we identified class S11 MYB transcription factors (TFs) as targets downstream of PaSTM. A cis-acting element, TTGACT, identified in the promoters of S11 MYB TFs was found to be important for PaSTM binding and activation. Overexpression of PaSTM or its downstream targets, PaMYB13, PaMYB14, and PaMYB17, enhanced de novo shoot regeneration in Arabidopsis, indicating the active role of the PaSTM-S11 PaMYB module in organogenesis. In summary, our data demonstrate that PaSTM is important for PLB development. The STM-S11 MYB regulatory module is evolutionarily conserved and may regulate shoot or shoot-related organ development in plants.
Collapse
Affiliation(s)
| | - Jhun-Chen Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Pou-Yi Chang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
82
|
Varapparambath V, Mathew MM, Shanmukhan AP, Radhakrishnan D, Kareem A, Verma S, Ramalho JJ, Manoj B, Vellandath AR, Aiyaz M, Radha RK, Landge AN, Mähönen AP, Heisler MG, Weijers D, Prasad K. Mechanical conflict caused by a cell-wall-loosening enzyme activates de novo shoot regeneration. Dev Cell 2022; 57:2063-2080.e10. [PMID: 36002002 DOI: 10.1016/j.devcel.2022.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/10/2022] [Accepted: 07/27/2022] [Indexed: 01/02/2023]
Abstract
Cellular heterogeneity is a hallmark of multicellular organisms. During shoot regeneration from undifferentiated callus, only a select few cells, called progenitors, develop into shoot. How these cells are selected and what governs their subsequent progression to a patterned organ system is unknown. Using Arabidopsis thaliana, we show that it is not just the abundance of stem cell regulators but rather the localization pattern of polarity proteins that predicts the progenitor's fate. A shoot-promoting factor, CUC2, activated the expression of the cell-wall-loosening enzyme, XTH9, solely in a shell of cells surrounding the progenitor, causing different mechanical stresses in these cells. This mechanical conflict then activates cell polarity in progenitors to promote meristem formation. Interestingly, genetic or physical perturbations to cells surrounding the progenitor impaired the progenitor and vice versa. These suggest a feedback loop between progenitors and their neighbors for shoot regeneration in the absence of tissue-patterning cues.
Collapse
Affiliation(s)
- Vijina Varapparambath
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | - Mabel Maria Mathew
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India.
| | - Anju Pallipurath Shanmukhan
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | | | - Abdul Kareem
- IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | - Shubham Verma
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India
| | - João Jacob Ramalho
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Bejoy Manoj
- IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | | | - Mohammed Aiyaz
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | | | | | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Marcus G Heisler
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Kalika Prasad
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India.
| |
Collapse
|
83
|
Liang Y, Heyman J, Xiang Y, Vandendriessche W, Canher B, Goeminne G, De Veylder L. The wound-activated ERF15 transcription factor drives Marchantia polymorpha regeneration by activating an oxylipin biosynthesis feedback loop. SCIENCE ADVANCES 2022; 8:eabo7737. [PMID: 35960801 PMCID: PMC9374346 DOI: 10.1126/sciadv.abo7737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The regenerative potential in response to wounding varies widely among species. Within the plant lineage, the liverwort Marchantia polymorpha displays an extraordinary regeneration capacity. However, its molecular pathways controlling the initial regeneration response are unknown. Here, we demonstrate that the MpERF15 transcription factor gene is instantly activated after wounding and is essential for gemmaling regeneration following tissue incision. MpERF15 operates both upstream and downstream of the MpCOI1 oxylipin receptor by controlling the expression of oxylipin biosynthesis genes. The resulting rise in the oxylipin dinor-12-oxo-phytodienoic acid (dn-OPDA) levels results in an increase in gemma cell number and apical notch organogenesis, generating highly disorganized and compact thalli. Our data pinpoint MpERF15 as a key factor activating an oxylipin biosynthesis amplification loop after wounding, which eventually results in reactivation of cell division and regeneration. We suggest that the genetic networks controlling oxylipin biosynthesis in response to wounding might have been reshuffled over evolution.
Collapse
Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Yanli Xiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Wiske Vandendriessche
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Balkan Canher
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| |
Collapse
|
84
|
Yang S, de Haan M, Mayer J, Janacek DP, Hammes UZ, Poppenberger B, Sieberer T. A novel chemical inhibitor of polar auxin transport promotes shoot regeneration by local enhancement of HD-ZIP III transcription. THE NEW PHYTOLOGIST 2022; 235:1111-1128. [PMID: 35491431 DOI: 10.1111/nph.18196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
De novo shoot organogenesis is a prerequisite for numerous applications in plant research and breeding but is often a limiting factor, for example, in genome editing approaches. Class III homeodomain-leucine zipper (HD-ZIP III) transcription factors have been characterized as crucial regulators of shoot specification, however up-stream components controlling their activity during shoot regeneration are only partially identified. In a chemical genetic screen, we isolated ZIC2, a novel activator of HD-ZIP III activity. Using molecular, physiological and hormone transport analyses in Arabidopsis and sunflower (Helianthus annuus), we examined the molecular mechanism by which the drug promotes HD-ZIP III expression. ZIC2-dependent upregulation of HD-ZIP III transcription promotes shoot regeneration in Arabidopsis and is accompanied by the induction of shoot specifying factors WUS and RAP2.6L and a subset of cytokinin biosynthesis enzymes. ZIC2's effect on HD-ZIP III expression and regeneration is based on its ability to limit polar auxin transport. We further provide evidence that chemical modulation of auxin efflux can enhance de novo shoot formation in the regeneration recalcitrant species sunflower. Activation of HD-ZIP III transcription during shoot regeneration depends on the local distribution of auxin and chemical modulation of auxin transport can be used to overcome poor shoot organogenesis in tissue culture.
Collapse
Affiliation(s)
- Saiqi Yang
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Marjolein de Haan
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Julius Mayer
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Dorina P Janacek
- Plant Systems Biology, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Ulrich Z Hammes
- Plant Systems Biology, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Tobias Sieberer
- Research Unit Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| |
Collapse
|
85
|
Lian Z, Nguyen CD, Liu L, Wang G, Chen J, Wang S, Yi G, Wilson S, Ozias‐Akins P, Gong H, Huo H. Application of developmental regulators to improve in planta or in vitro transformation in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1622-1635. [PMID: 35524453 PMCID: PMC9342618 DOI: 10.1111/pbi.13837] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 05/08/2023]
Abstract
Plant genetic transformation is a crucial step for applying biotechnology such as genome editing to basic and applied plant science research. Its success primarily relies on the efficiency of gene delivery into plant cells and the ability to regenerate transgenic plants. In this study, we have examined the effect of several developmental regulators (DRs), including PLETHORA (PLT5), WOUND INDUCED DEDIFFERENTIATION 1 (WIND1), ENHANCED SHOOT REGENERATION (ESR1), WUSHEL (WUS) and a fusion of WUS and BABY-BOOM (WUS-P2A-BBM), on in planta transformation through injection of Agrobacterium tumefaciens in snapdragons (Antirrhinum majus). The results showed that PLT5, WIND1 and WUS promoted in planta transformation of snapdragons. An additional test of these three DRs on tomato (Solanum lycopersicum) further demonstrated that the highest in planta transformation efficiency was observed from PLT5. PLT5 promoted calli formation and regeneration of transformed shoots at the wound positions of aerial stems, and the transgene was stably inherited to the next generation in snapdragons. Additionally, PLT5 significantly improved the shoot regeneration and transformation in two Brassica cabbage varieties (Brassica rapa) and promoted the formation of transgenic calli and somatic embryos in sweet pepper (Capsicum annum) through in vitro tissue culture. Despite some morphological alternations, viable seeds were produced from the transgenic Bok choy and snapdragons. Our results have demonstrated that manipulation of PLT5 could be an effective approach for improving in planta and in vitro transformation efficiency, and such a transformation system could be used to facilitate the application of genome editing or other plant biotechnology application in modern agriculture.
Collapse
Affiliation(s)
- Zhaoyuan Lian
- Department of Environmental HorticultureMid‐Florida Research and Education CenterUniversity of FloridaApopkaFLUSA
| | - Chi Dinh Nguyen
- Department of Environmental HorticultureMid‐Florida Research and Education CenterUniversity of FloridaApopkaFLUSA
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life SciencesHubei UniversityWuhanChina
| | - Guiluan Wang
- Department of Environmental HorticultureMid‐Florida Research and Education CenterUniversity of FloridaApopkaFLUSA
| | - Jianjun Chen
- Department of Environmental HorticultureMid‐Florida Research and Education CenterUniversity of FloridaApopkaFLUSA
| | - Songhu Wang
- School of HorticultureAnhui Agricultural UniversityHefeiChina
| | - Ganjun Yi
- Guangdong Academy of Agricultural ScienceGuangzhouChina
| | - Sandra Wilson
- Department of Environmental HorticultureUniversity of FloridaGainesvilleFLUSA
| | - Peggy Ozias‐Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics and GenomicsUniversity of GeorgiaTiftonGAUSA
| | - Haijun Gong
- Shaanxi Engineering Research Center for Vegetables, College of HorticultureNorthwest Agricultural and Forestry UniversityYanglingChina
| | - Heqiang Huo
- Department of Environmental HorticultureMid‐Florida Research and Education CenterUniversity of FloridaApopkaFLUSA
| |
Collapse
|
86
|
Okazaki K, Koike I, Kera S, Yamaguchi K, Shigenobu S, Shimomura K, Umehara M. Gene expression profiling before and after internode culture for adventitious shoot formation in ipecac. BMC PLANT BIOLOGY 2022; 22:361. [PMID: 35869421 PMCID: PMC9308184 DOI: 10.1186/s12870-022-03756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND In ipecac (Carapichea ipecacuanha (Brot.) L. Andersson), adventitious shoots can be induced simply by placing internodal segments on phytohormone-free culture medium. The shoots form locally on the epidermis of the apical region of the segments, but not the basal region. Levels of endogenous auxin and cytokinin transiently increase in the segments after 1 week of culture. RESULTS Here, we conducted RNA-seq analysis to compare gene expression patterns in apical and basal regions of segments before culture and after 1 week of culture for adventitious shoot formation. The results revealed 8987 differentially expressed genes in a de novo assembly of 76,684 genes. Among them, 276 genes were upregulated in the apical region after 1 week of culture relative to before culture and the basal region after 1 week of culture. These genes include 18 phytohormone-response genes and shoot-formation-related genes. Validation of the gene expression by quantitative real-time PCR assay confirmed that the expression patterns were similar to those of the RNA-seq data. CONCLUSIONS The transcriptome data show that expression of cytokinin biosynthesis genes is induced along with the acquisition of cellular pluripotency and the initiation of cell division by wounding in the apical region of internodal segments, that trigger adventitious shoot formation without callusing.
Collapse
Affiliation(s)
- Karin Okazaki
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Imari Koike
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Sayuri Kera
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Katushi Yamaguchi
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Koichiro Shimomura
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Mikihisa Umehara
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan.
- Department of Applied Biosciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan.
| |
Collapse
|
87
|
Liu W, Zhang Y, Fang X, Tran S, Zhai N, Yang Z, Guo F, Chen L, Yu J, Ison MS, Zhang T, Sun L, Bian H, Zhang Y, Yang L, Xu L. Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses. PLANT COMMUNICATIONS 2022; 3:100306. [PMID: 35605192 PMCID: PMC9284295 DOI: 10.1016/j.xplc.2022.100306] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Detached Arabidopsis thaliana leaves can regenerate adventitious roots, providing a platform for studying de novo root regeneration (DNRR). However, the comprehensive transcriptional framework of DNRR remains elusive. Here, we provide a high-resolution landscape of transcriptome reprogramming from wound response to root organogenesis in DNRR and show key factors involved in DNRR. Time-lapse RNA sequencing (RNA-seq) of the entire leaf within 12 h of leaf detachment revealed rapid activation of jasmonate, ethylene, and reactive oxygen species (ROS) pathways in response to wounding. Genetic analyses confirmed that ethylene and ROS may serve as wound signals to promote DNRR. Next, time-lapse RNA-seq within 5 d of leaf detachment revealed the activation of genes involved in organogenesis, wound-induced regeneration, and resource allocation in the wounded region of detached leaves during adventitious rooting. Genetic studies showed that BLADE-ON-PETIOLE1/2, which control aboveground organs, PLETHORA3/5/7, which control root organogenesis, and ETHYLENE RESPONSE FACTOR115, which controls wound-induced regeneration, are involved in DNRR. Furthermore, single-cell RNA-seq data revealed gene expression patterns in the wounded region of detached leaves during adventitious rooting. Overall, our study not only provides transcriptome tools but also reveals key factors involved in DNRR from detached Arabidopsis leaves.
Collapse
Affiliation(s)
- Wu Liu
- 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, 300 Fenglin Road, Shanghai 200032, China
| | - Yuyun Zhang
- 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, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Xing Fang
- 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, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Sorrel Tran
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - 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, 300 Fenglin Road, Shanghai 200032, China
| | - Zhengfei Yang
- 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, 300 Fenglin Road, Shanghai 200032, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Fu Guo
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
| | - Lyuqin Chen
- 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, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Jie Yu
- 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, 300 Fenglin Road, Shanghai 200032, China
| | - Madalene S Ison
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Teng Zhang
- 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, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijing Zhang
- 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, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Li Yang
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA.
| | - 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, 300 Fenglin Road, Shanghai 200032, China.
| |
Collapse
|
88
|
Conifer Biotechnology: An Overview. FORESTS 2022. [DOI: 10.3390/f13071061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The peculiar characteristics of conifers determine the difficulty of their study and their great importance from various points of view. However, their study faces numerous important scientific, methodological, cultural, economic, social, and legal challenges. This paper presents an approach to several of those challenges and proposes a multidisciplinary scientific perspective that leads to a holistic understanding of conifers from the perspective of the latest technical, computer, and scientific advances. This review highlights the deep connection that all scientific contributions to conifers can have in each other as fully interrelated communicating vessels.
Collapse
|
89
|
Asghar S, Xiong Y, Che M, Fan X, Li H, Wang Y, Xu X, Li W, Han Z. Transcriptome analysis reveals the effects of strigolactone on shoot regeneration of apple. PLANT CELL REPORTS 2022; 41:1613-1626. [PMID: 35680714 DOI: 10.1007/s00299-022-02882-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
We have demonstrated that strigolactone inhibitor, Tis108, could be used to improve shoot regeneration of apple, and provided insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Lack of an efficient transformation system largely stagnated the application of transgenic and CRISPR technology in apple rootstock. High shoot regeneration ability is an important basis for establishing an effective transformation system. In this study, we first demonstrated the inhibitory effects of strigolactones on the adventitious shoot formation of apple rootstock M26. Next, we successfully verified that strigolactone-biosynthesis inhibitor, Tis108, could be used to improve the shoot regeneration of woody plants. Our results also suggest strigolactone-biosynthesis gene, MdCCD7, can be a target gene for biotechnological improvements of shoot regeneration capacity. Furthermore, we have employed transcriptome analysis to reveal the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Differentially expressed genes associated with photosynthesis, secondary growth, and organ development were identified. WGCNA suggests SLs might affect shoot regeneration through interaction with other hormones, especially, auxin, cytokinin, and ethylene. We were able to identify important candidate genes mediating the cross-talk between strigolactone and other hormones during the process of adventitious shoot formation. Overall, our findings not only propose a useful chemical for improving shoot regeneration in practice but also provide insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation.
Collapse
Affiliation(s)
- Sumeera Asghar
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yao Xiong
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Meng Che
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xingqiang Fan
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Hui Li
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wei Li
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
90
|
Long Y, Yang Y, Pan G, Shen Y. New Insights Into Tissue Culture Plant-Regeneration Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:926752. [PMID: 35845646 PMCID: PMC9280033 DOI: 10.3389/fpls.2022.926752] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/31/2022] [Indexed: 05/08/2023]
Abstract
Plant regeneration occurs when plants repair or replace damaged structures based on the totipotency and pluripotency of their cells. Tissue culture is one of the most widely used regenerative technologies. Recently, a series of breakthroughs were made in the study of plant regeneration. This review summarizes two regenerative pathways in tissue culture: somatic embryogenesis and de novo organogenesis. Furthermore, we review the environmental factors influencing plant regeneration from explant sources, basal culture medium, plant growth regulators, and light/dark treatment. Additionally, we analyse the molecular mechanisms underlying two pathways. This knowledge will promote an understanding of the fundamental principles of plant regeneration from precursor cells and lay a solid foundation for applying plant micropropagation and genetic modification.
Collapse
Affiliation(s)
- Yun Long
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Yun Yang
- Nanchong Academy of Agricultural Sciences, Nanchong, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
91
|
Zheng B, Liu J, Gao A, Chen X, Gao L, Liao L, Luo B, Ogutu CO, Han Y. Epigenetic reprogramming of H3K27me3 and DNA methylation during leaf-to-callus transition in peach. HORTICULTURE RESEARCH 2022; 9:uhac132. [PMID: 35937864 PMCID: PMC9350832 DOI: 10.1093/hr/uhac132] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/29/2022] [Indexed: 05/30/2023]
Abstract
Plant tissues are capable of developing unorganized cell masses termed calluses in response to the appropriate combination of auxin and cytokinin. Revealing the potential epigenetic mechanisms involved in callus development can improve our understanding of the regeneration process of plant cells, which will be beneficial for overcoming regeneration recalcitrance in peach. In this study, we report on single-base resolution mapping of DNA methylation and reprogramming of the pattern of trimethylation of histone H3 at lysine 27 (H3K27me3) at the genome-wide level during the leaf-to-callus transition in peach. Overall, mCG and mCHH were predominant at the genome-wide level and mCG was predominant in genic regions. H3K27me3 deposition was mainly detected in the gene body and at the TSS site, and GAGA repetitive sequences were prone to recruit H3K27me3 modification. H3K27me3 methylation was negatively correlated with gene expression. In vitro culture of leaf explants was accompanied by DNA hypomethylation and H3K27me3 demethylation, which could activate auxin- and cytokinin-related regulators to induce callus development. The DNA methylation inhibitor 5-azacytidine could significantly increase callus development, while the H3K27me3 demethylase inhibitor GSK-J4 dramatically reduced callus development. These results demonstrate the roles of DNA methylation and H3K27me3 modification in mediating chromatin status during callus development. Our study provides new insights into the epigenetic mechanisms through which differentiated cells acquire proliferative competence to induce callus development in plants.
Collapse
Affiliation(s)
- Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingjing Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Anqi Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xiaomei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Lingling Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Binwen Luo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yuepeng Han
- Corresponding author. E-mail:
Equal contribution
| |
Collapse
|
92
|
Wang G, Zhang Y, Li C, Wang X, Fletcher JC. Signaling peptides direct the art of rebirth. TRENDS IN PLANT SCIENCE 2022; 27:516-519. [PMID: 35397996 DOI: 10.1016/j.tplants.2022.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Signaling peptide-mediated cell-cell communication is crucial for plant growth, development, and adaptive responses to environmental stimuli. Given the prominent roles signaling peptides play in stem cell homeostasis, we propose investigating their impact on plant regeneration, which requires cellular reprogramming of differentiated cells to stem cells and establishment of nascent meristems.
Collapse
Affiliation(s)
- Guodong Wang
- National Engineering Laboratory for Endangered Medicinal Resources Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Chen Li
- Laboratory of Medicinal Plant, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xuening Wang
- National Engineering Laboratory for Endangered Medicinal Resources Development in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Jennifer C Fletcher
- Plant Gene Expression Center, USDA-ARS/UC Berkeley, Albany, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
| |
Collapse
|
93
|
Shi QF, Long JM, Yin ZP, Jiang N, Feng MQ, Zheng B, Guo WW, Wu XM. miR171 modulates induction of somatic embryogenesis in citrus callus. PLANT CELL REPORTS 2022; 41:1403-1415. [PMID: 35381869 DOI: 10.1007/s00299-022-02865-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Overexpression of miR171 restored SE competence in the recalcitrant citrus callus, and inhibition of miR171 function weakened SE competence in the strongly embryogenic citrus callus. Somatic embryogenesis (SE) is an important way of in vitro regeneration for plants. For perennial woody crops such as citrus, embryogenic callus is usually induced from unfertilized aborted ovules and widely used in biotechnology aided breeding. However, SE capacity always declines in callus during subculture, which makes regeneration difficult and hinders the application of biotechnology. We previously found that miR171 may be a regulator of SE in citrus, based on the abundant expression of csi-miR171c in the embryogenic callus and during SE of citrus. Here, we report that miR171 promotes SE and is required for SE in citrus. Overexpression of miR171 restored SE competence in the recalcitrant callus of 'Guoqing No.1' Satsuma mandarin (G1), whereas inhibition of miR171 function by Short Tandem Target Mimic (STTM) weakened SE competence in the strongly embryogenic callus of 'Valencia' sweet orange (V). The comparative transcriptomic analysis in miR171 overexpressed callus line (OE) and the wild type callus (WT) indicated that overexpression of miR171 decreased the expression level of its SCARECROW-LIKE (CsSCL) targets, and activated stress response related biological processes and metabolic processes that are required for cell differentiation. However, CsSCLs were up-regulated in the OE callus during SE induction process, which activated the cell division and developmental processes that are required for embryogenesis progress. Our results validate the function of miR171 in regulation of SE and reveal the biological responses provoked by miR171 in citrus that may promote SE.
Collapse
Affiliation(s)
- Qiao-Fang Shi
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian-Mei Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhao-Ping Yin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nan Jiang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meng-Qi Feng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
94
|
Kübler IC, Kretzschmar J, Brankatschk M, Sandoval-Guzmán T. Local problems need global solutions - the metabolic needs of regenerating organisms. Wound Repair Regen 2022; 30:652-664. [PMID: 35596643 DOI: 10.1111/wrr.13029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/03/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022]
Abstract
The vast majority of species that belong to the plant or animal kingdom evolved with two main strategies to counter tissue damage - scar formation and regeneration. Whereas scar formation provides a fast and cost-effective repair to exit life-threatening conditions, complete tissue regeneration is time-consuming and requires vast resources to reinstall functionality of affected organs or structures. Local environments in wound healing are widely studied and findings have provided important biomedical applications. Less well understood are organismic physiological parameters and signaling circuits essential to maintain effective tissue repair. Here, we review accumulated evidence that positions the interplay of local and systemic changes in metabolism as essential variables modulating the injury response. We particularly emphasize the role of lipids and lipid-like molecules as significant components long overlooked. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Ines C Kübler
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Jenny Kretzschmar
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Marko Brankatschk
- Department of Molecular, Cell and Developmental Biology, Technische Universität Dresden, Germany
| | - Tatiana Sandoval-Guzmán
- Department of Internal Medicine III, Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden of Helmholtz Centre Munich, at University Clinic Carl Gustav Carus, TU Dresden Faculty of Medicine, Dresden, Germany
| |
Collapse
|
95
|
Yue J, Dong Y, Liu S, Jia Y, Li C, Wang Z, Gong S. Integrated Proteomic and Metabolomic Analyses Provide Insights Into Acquisition of Embryogenic Ability in Agapanthus praecox. FRONTIERS IN PLANT SCIENCE 2022; 13:858065. [PMID: 35665191 PMCID: PMC9158531 DOI: 10.3389/fpls.2022.858065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Somatic embryogenesis (SE) is an ideal model for plant cell totipotency. Transition from somatic cells to embryogenic cells is the key to SE. The poor frequency of embryogenic callus (EC) induction has limited the application of SE in many plants, such as Agapanthus praecox. We performed large-scale, quantitative proteomic and metabolomic analyses with different callus differentiation directions (SE and organogenesis) and stages (initial SE and repetitive SE) to better understand the morphological, physiological, and molecular characteristics of the acquisition of embryogenic ability in A. praecox. Integrated proteomic and metabolomic analyses suggested that callus differentiation direction was potentially regulated by pathways related to carbohydrate and energy metabolism (fatty acid metabolism, pyruvate metabolism, glycolysis/gluconeogenesis, pentose and glucuronate interconversions, starch and sucrose metabolism, galactose metabolism, carbon fixation pathways in prokaryotes, carbohydrate digestion and absorption, and fructose and mannose metabolism), chromatin accessibility and DNA methylation, reactive oxygen species responses and resistance (ascorbate and aldarate metabolism), and plant hormonal signaling. As a validation, we found that carbon source combination and plant hormone regulation in the culture medium significantly affected the acquisition of embryogenic ability, thereby inducing EC. Interestingly, plant hormonal signaling-related genes showed different expression patterns significantly when callus cultured with different carbon sources. Thus, our results suggested that energy supply and hormone signal transduction seemed to cooperatively contribute to the activation of embryogenic ability. Altogether, this study revealed valuable information regarding the molecular and biochemical changes that occurred during EC induction and provided valuable foundation for comprehensive understanding of the mechanisms associated with SE and organogenesis in A. praecox.
Collapse
Affiliation(s)
- Jianhua Yue
- School of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Yan Dong
- School of Forestry, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Songhu Liu
- School of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Yanan Jia
- College of Plant Science, Tarim University, Alar, China
| | - Chaoxin Li
- School of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Zhiyong Wang
- School of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Shoufu Gong
- School of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, China
| |
Collapse
|
96
|
Lambolez A, Kawamura A, Takahashi T, Rymen B, Iwase A, Favero DS, Ikeuchi M, Suzuki T, Cortijo S, Jaeger KE, Wigge PA, Sugimoto K. Warm Temperature Promotes Shoot Regeneration in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2022; 63:618-634. [PMID: 35157760 DOI: 10.1093/pcp/pcac017] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we find that warm temperature promotes both callus formation and shoot regeneration in Arabidopsis thaliana. We show that such an increase in shoot regenerative capacity at higher temperatures correlates with the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1) encoding a transcription factor involved in shoot meristem formation and YUCCAs (YUCs) encoding auxin biosynthesis enzymes. ChIP-sequencing analyses further reveal that histone variant H2A.Z is enriched on these loci at 17°C, while its occupancy is reduced by an increase in ambient temperature to 27°C. Moreover, we provide genetic evidence to demonstrate that H2A.Z acts as a repressor of de novo shoot organogenesis since H2A.Z-depleted mutants display enhanced shoot regeneration. This study thus uncovers a new chromatin-based mechanism that influences hormone-induced regeneration and additionally highlights incubation temperature as a key parameter for optimizing in vitro tissue culture.
Collapse
Affiliation(s)
- Alice Lambolez
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyō-ku, Tōkyō 113-8654, Japan
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Tatsuya Takahashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Bart Rymen
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084, France
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - David S Favero
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biology, Faculty of Science, Niigata University, Ikarashi, Niigata 950-2181, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Sandra Cortijo
- UMR5004 Biochimie et Physiologie Moléculaire des Plantes, Université de Montpellier, CNRS, INRAE, Institut Agro, 2 place Pierre Viala, Montpellier 34060, France
| | - Katja E Jaeger
- Leibniz-Institut für Gemüse- und Zierpflanzenbau (IGZ) e.V., Theodor-Echtermeyer-Weg 1, Großbeeren 14979, Germany
| | - Philip A Wigge
- Leibniz-Institut für Gemüse- und Zierpflanzenbau (IGZ) e.V., Theodor-Echtermeyer-Weg 1, Großbeeren 14979, Germany
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyō-ku, Tōkyō 113-8654, Japan
| |
Collapse
|
97
|
Popov VN, Syromyatnikov MY, Franceschi C, Moskalev AA, Krutovsky KV, Krutovsky KV. Genetic mechanisms of aging in plants: What can we learn from them? Ageing Res Rev 2022; 77:101601. [PMID: 35278719 DOI: 10.1016/j.arr.2022.101601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/03/2022] [Accepted: 03/02/2022] [Indexed: 12/18/2022]
Abstract
Plants hold all records in longevity. Their aging is a complex process. In the presented review, we analyzed published data on various aspects of plant aging with focus on any inferences that could shed a light on aging in animals and help to fight it in human. Plant aging can be caused by many factors, such as telomere depletion, genomic instability, loss of proteostasis, changes in intercellular interaction, desynchronosis, autophagy misregulation, epigenetic changes and others. Plants have developed a number of mechanisms to increase lifespan. Among these mechanisms are gene duplication ("genetic backup"), the active work of telomerases, abundance of meristematic cells, capacity of maintaining the meristems permanently active and continuous activity of phytohormones. Plant aging usually occurs throughout the whole perennial life, but could be also seasonal senescence. Study of causes for seasonal aging can also help to uncover the mechanisms of plant longevity. The influence of different factors such as microbiome communities, glycation, alternative oxidase activity, mitochondrial dysfunction on plant longevity was also reviewed. Adaptive mechanisms of long-lived plants are considered. Further comparative study of the mechanisms underlying longevity of plants is necessary. This will allow us to reach a potentially new level of understanding of the aging process of plants.
Collapse
|
98
|
Nicolas A, Laufs P. Meristem Initiation and de novo Stem Cell Formation. FRONTIERS IN PLANT SCIENCE 2022; 13:891228. [PMID: 35557739 PMCID: PMC9087721 DOI: 10.3389/fpls.2022.891228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Plant aerial development relies on meristem activity which ensures main body plant axis development during plant life. While the shoot apical meristem (SAM) formed in the embryo only contributes to the main stem, the branched structure observed in many plants relies on axillary meristems (AMs) formed post-embryonically. These AMs initiate from a few cells of the leaf axil that retain meristematic characteristics, increase in number, and finally organize into a structure similar to the SAM. In this review, we will discuss recent findings on de novo establishment of a stem cell population and its regulatory niche, a key step essential for the indeterminate fate of AMs. We stress that de novo stem cell formation is a progressive process, which starts with a transient regulatory network promoting stem cell formation and that is different from the one acting in functional meristems. This transient stage can be called premeristems and we discuss whether this concept can be extended to the formation of meristems other than AMs.
Collapse
Affiliation(s)
- Antoine Nicolas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- Université Paris-Saclay, Orsay, France
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| |
Collapse
|
99
|
Shang GD, Xu ZG, Wan MC, Wang FX, Wang JW. FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data. BMC Genomics 2022; 23:272. [PMID: 35392802 PMCID: PMC8988339 DOI: 10.1186/s12864-022-08506-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets. RESULTS Here, we introduce FindIT2 (Find Influential TFs and Targets), an R/Bioconductor package for annotating and processing high-throughput multi-omics data. FindIT2 supports a complete framework for annotating ChIP-seq/ATAC-seq peaks, identifying TF targets by the combination of ChIP-seq and RNA-seq datasets, and inferring influential TFs based on different types of data input. Moreover, benefited from the annotation framework based on Bioconductor, FindIT2 can be applied to any species with genomic annotations, which is particularly useful for the non-model species that are less well-studied. CONCLUSION FindIT2 provides a user-friendly and flexible framework to generate results at different levels according to the richness of the annotation information of user's species. FindIT2 is compatible with all the operating systems and is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor ( https://bioconductor.org/packages/devel/bioc/html/FindIT2.html ).
Collapse
Affiliation(s)
- Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China
| | - Mu-Chun Wan
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Fu-Xiang Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China.
- University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
100
|
Iwase A, Takebayashi A, Aoi Y, Favero DS, Watanabe S, Seo M, Kasahara H, Sugimoto K. 4-Phenylbutyric acid promotes plant regeneration as an auxin by being converted to phenylacetic acid via an IBR3-independent pathway. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:51-58. [PMID: 35601015 PMCID: PMC9080989 DOI: 10.5511/plantbiotechnology.21.1224b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/24/2021] [Indexed: 05/07/2023]
Abstract
4-Phenylbutyric acid (4PBA) is utilized as a drug to treat urea cycle disorders and is also being studied as a potential anticancer drug that acts via its histone deacetylase (HDAC) inhibitor activity. During a search to find small molecules that affect plant regeneration in Arabidopsis, we found that 4PBA treatment promotes this process by mimicking the effect of exogenous auxin. Specifically, plant tissue culture experiments revealed that a medium containing 4PBA enhances callus formation and subsequent shoot regeneration. Analyses with auxin-responsive or cytokinin-responsive marker lines demonstrated that 4PBA specifically enhances AUXIN RESPONSE FACTOR (ARF)-dependent auxin responses. Our western blot analyses showed that 4PBA treatment does not enhance histone acetylation in Arabidopsis, in contrast to butyric acid and trichostatin A, other chemicals often used as HDAC inhibitors, suggesting this mechanism of action does not explain the observed effect of 4PBA on regeneration. Finally, mass spectroscopic analysis and genetic approaches uncovered that 4PBA in Arabidopsis plants is converted to phenylacetic acid (PAA), a known natural auxin, in a manner independent of peroxisomal IBR3-related β-oxidation. This study demonstrates that 4PBA application promotes regeneration in explants via its auxin activity and has potential applications to not only plant tissue culture engineering but also research on the plant β-oxidation pathway.
Collapse
Affiliation(s)
- Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
- E-mail: Tel: +81-45-503-9570 Fax: +81-45-503-9591
| | - Arika Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Aoi
- Department of Biological Production Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Watanabe
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Kasahara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- E-mail: Tel: +81-45-503-9570 Fax: +81-45-503-9591
| |
Collapse
|