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Denjalli I, Knieper M, Uthoff J, Vogelsang L, Kumar V, Seidel T, Dietz KJ. The centrality of redox regulation and sensing of reactive oxygen species in abiotic and biotic stress acclimatization. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4494-4511. [PMID: 38329465 DOI: 10.1093/jxb/erae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
During land plant evolution, the number of genes encoding for components of the thiol redox regulatory network and the generator systems of reactive oxygen species (ROS) expanded, tentatively indicating that they have a role in tailored environmental acclimatization. This hypothesis has been validated both experimentally and theoretically during the last few decades. Recent developments of dynamic redox-sensitive GFP (roGFP)-based in vivo sensors for H2O2 and the redox potential of the glutathione pool have paved the way for dissecting the kinetics changes that occur in these crucial parameters in response to environmental stressors. The versatile cellular redox sensory and response regulatory system monitors alterations in redox metabolism and controls the activity of redox target proteins, and thereby affects most, if not all, cellular processes ranging from transcription to translation and metabolism. This review uses examples to describe the role of the redox- and ROS-dependent regulatory network in realising the appropriate responses to diverse environmental stresses. The selected case studies concern different environmental challenges, namely excess excitation energy, the heavy metal cadmium and the metalloid arsenic, nitrogen or phosphate shortages as examples for nutrient deficiency, wounding, and nematode infestation. Each challenge affects the redox-regulatory and ROS network, but our present state of knowledge also points toward pressing questions that remain open in relation to the translation of redox regulation to environmental acclimatization.
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Affiliation(s)
- Ibadete Denjalli
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Madita Knieper
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Center of Biotechnology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Jana Uthoff
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Lara Vogelsang
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Center of Biotechnology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Vijay Kumar
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Thorsten Seidel
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Center of Biotechnology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
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2
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Coomey JH, MacKinnon KJM, McCahill IW, Khahani B, Handakumbura PP, Trabucco GM, Mazzola J, Leblanc NA, Kheam R, Hernandez-Romero M, Barry K, Liu L, Lee JE, Vogel JP, O’Malley RC, Chambers JJ, Hazen SP. Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression. QUANTITATIVE PLANT BIOLOGY 2024; 5:e5. [PMID: 38774130 PMCID: PMC11106548 DOI: 10.1017/qpb.2024.5] [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: 08/09/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 05/24/2024]
Abstract
Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.
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Affiliation(s)
- Joshua H. Coomey
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Kirk J.-M. MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Ian W. McCahill
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Bahman Khahani
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Pubudu P. Handakumbura
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Gina M. Trabucco
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Jessica Mazzola
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | | | - Rithany Kheam
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | - Miriam Hernandez-Romero
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lifeng Liu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ji E. Lee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John P. Vogel
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan C. O’Malley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James J. Chambers
- Institute for Applied Life Science, University of Massachusetts, Amherst, MA, USA
| | - Samuel P. Hazen
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
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Takou M, Bellis ES, Lasky JR. Predicting gene expression responses to environment in Arabidopsis thaliana using natural variation in DNA sequence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591174. [PMID: 38712066 PMCID: PMC11071634 DOI: 10.1101/2024.04.25.591174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The evolution of gene expression responses are a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved for cis regulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlying cis- regulatory genotype to phenotype map. We tested this approach using cold-responsive transcriptome profiles in 5 diverse Arabidopsis thaliana accessions. We first tested for evidence that cis regulation plays a role in environmental response, finding 14 and 15 motifs that were significantly enriched within the up- and down-stream regions of cold-responsive differentially regulated genes (DEGs). We next applied convolutional neural networks (CNNs), which learn de novo cis- regulatory motifs in DNA sequences to predict expression response to environment. We found that CNNs predicted differential expression with moderate accuracy, with evidence that predictions were hindered by biological complexity of regulation and the large potential regulatory code. Overall, DEGs between specific environments can be predicted based on variation in cis- regulatory sequences, although more information needs to be incorporated and better models may be required.
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Castro-Camba R, Neves M, Correia S, Canhoto J, Vielba JM, Sánchez C. Ethylene Action Inhibition Improves Adventitious Root Induction in Adult Chestnut Tissues. PLANTS (BASEL, SWITZERLAND) 2024; 13:738. [PMID: 38475584 DOI: 10.3390/plants13050738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
Phase change refers to the process of maturation and transition from the juvenile to the adult stage. In response to this shift, certain species like chestnut lose the ability to form adventitious roots, thereby hindering the successful micropropagation of adult plants. While auxin is the main hormone involved in adventitious root formation, other hormones, such as ethylene, are also thought to play a role in its induction and development. In this study, experiments were carried out to determine the effects of ethylene on the induction and growth of adventitious roots. The analysis was performed in two types of chestnut microshoots derived from the same tree, a juvenile-like line with a high rooting ability derived from basal shoots (P2BS) and a line derived from crown branches (P2CR) with low rooting responses. By means of the application of compounds to modify ethylene content or inhibit its signalling, the potential involvement of this hormone in the induction of adventitious roots was analysed. Our results show that ethylene can modify the rooting competence of mature shoots, while the response in juvenile material was barely affected. To further characterise the molecular reasons underlying this maturation-derived shift in behaviour, specific gene expression analyses were developed. The findings suggest that several mechanisms, including ethylene signalling, auxin transport and epigenetic modifications, relate to the modulation of the rooting ability of mature chestnut microshoots and their recalcitrant behaviour.
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Affiliation(s)
- Ricardo Castro-Camba
- Department of Plant Production, Misión Biológica de Galicia, CSIC, Avda de Vigo s/n, 15705 Santiago de Compostela, Spain
| | - Mariana Neves
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- InnovPlantProtect CoLab, Estrada de Gil Vaz, 7350-478 Elvas, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Jesús M Vielba
- Department of Plant Production, Misión Biológica de Galicia, CSIC, Avda de Vigo s/n, 15705 Santiago de Compostela, Spain
| | - Conchi Sánchez
- Department of Plant Production, Misión Biológica de Galicia, CSIC, Avda de Vigo s/n, 15705 Santiago de Compostela, Spain
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Chen Y, Wang Z, Gao T, Huang Y, Li T, Jiang X, Liu Y, Gao L, Xia T. Deep learning and targeted metabolomics-based monitoring of chewing insects in tea plants and screening defense compounds. PLANT, CELL & ENVIRONMENT 2024; 47:698-713. [PMID: 37882465 DOI: 10.1111/pce.14749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Tea is an important cash crop that is often consumed by chewing pests, resulting in reduced yields and economic losses. It is important to establish a method to quickly identify the degree of damage to tea plants caused by leaf-eating insects and screen green control compounds. This study was performed through the combination of deep learning and targeted metabolomics, in vitro feeding experiment, enzymic analysis and transient genetic transformation. A small target damage detection model based on YOLOv5 with Transformer Prediction Head (TPH-YOLOv5) algorithm for the tea canopy level was established. Orthogonal partial least squares (OPLS) was used to analyze the correlation between the degree of damage and the phenolic metabolites. A potential defensive compound, (-)-epicatechin-3-O-caffeoate (EC-CA), was screened. In vitro feeding experiments showed that compared with EC and epicatechin gallate, Ectropis grisescens exhibited more significant antifeeding against EC-CA. In vitro enzymatic experiments showed that the hydroxycinnamoyl transferase (CsHCTs) recombinant protein has substrate promiscuity and can catalyze the synthesis of EC-CA. Transient overexpression of CsHCTs in tea leaves effectively reduced the degree of damage to tea leaves. This study provides important reference values and application prospects for the effective monitoring of pests in tea gardens and screening of green chemical control substances.
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Affiliation(s)
- Yifan Chen
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- Henan Key Laboratory of Tea Plant Biology, College of Life Science, Xinyang Normal University, Xinyang, China
| | - Zhenyu Wang
- Henan Key Laboratory of Tea Plant Biology, College of Life Science, Xinyang Normal University, Xinyang, China
| | - Tian Gao
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Yipeng Huang
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Tongtong Li
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaolan Jiang
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Yajun Liu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
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6
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McCahill IW, Khahani B, Probert CF, Flockhart EL, Abushal LT, Gregory GA, Zhang Y, Baumgart LA, O’Malley RC, Hazen SP. Shoring up the base: the development and regulation of cortical sclerenchyma in grass nodal roots. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577257. [PMID: 38352548 PMCID: PMC10862697 DOI: 10.1101/2024.01.25.577257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Plants depend on the combined action of a shoot-root-soil system to maintain their anchorage to the soil. Mechanical failure of any component of this system results in lodging, a permanent and irreversible inability to maintain vertical orientation. Models of anchorage in grass crops identify the compressive strength of roots near the soil surface as key determinant of resistance to lodging. Indeed, studies of disparate grasses report a ring of thickened, sclerenchyma cells surrounding the root cortex, present only at the base of nodal roots. Here, in the investigation of the development and regulation of this agronomically important trait, we show that development of these cells is uncoupled from the maturation of other secondary cell wall-fortified cells, and that cortical sclerenchyma wall thickening is stimulated by mechanical forces transduced from the shoot to the root. We also show that exogenous application of gibberellic acid stimulates thickening of lignified cell types in the root, including cortical sclerenchyma, but is not sufficient to establish sclerenchyma identity in cortex cells. Leveraging the ability to manipulate cortex development via mechanical stimulus, we show that cortical sclerenchyma development alters root mechanical properties and improves resistance to lodging. We describe transcriptome changes associated with cortical sclerenchyma development under both ambient and mechanically stimulated conditions and identify SECONDARY WALL NAC7 as a putative regulator of mechanically responsive cortex cell wall development at the root base.
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Affiliation(s)
- Ian W. McCahill
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Bahman Khahani
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | | | | | - Logayn T. Abushal
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Greg A. Gregory
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Yu Zhang
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Leo A. Baumgart
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan C. O’Malley
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Samuel P. Hazen
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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7
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Mendieta JP, Sangra A, Yan H, Minow MAA, Schmitz RJ. Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1486-1499. [PMID: 37309871 PMCID: PMC10598807 DOI: 10.1111/tpj.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with the inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall has limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Advances in single-cell epigenomics have revolutionized the field of identifying cell-type-specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single-cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single-cell research, challenges, and common pitfalls in the analysis of plant single-cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single-cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.
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Affiliation(s)
| | - Ankush Sangra
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Mark A A Minow
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
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Bao Y, Wei Y, Liu Y, Gao J, Cheng S, Liu G, You Q, Liu P, Lu Q, Li P, Zhang S, Hu N, Han Y, Liu S, Wu Y, Yang Q, Li Z, Ao G, Liu F, Wang K, Jiang J, Zhang T, Zhang W, Peng R. Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton. BMC Biol 2023; 21:165. [PMID: 37525156 PMCID: PMC10391996 DOI: 10.1186/s12915-023-01665-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/18/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The development of cotton fiber is regulated by the orchestrated binding of regulatory proteins to cis-regulatory elements associated with developmental genes. The cis-trans regulatory dynamics occurred throughout the course of cotton fiber development are elusive. Here we generated genome-wide high-resolution DNase I hypersensitive sites (DHSs) maps to understand the regulatory mechanisms of cotton ovule and fiber development. RESULTS We generated DNase I hypersensitive site (DHS) profiles from cotton ovules at 0 and 3 days post anthesis (DPA) and fibers at 8, 12, 15, and 18 DPA. We obtained a total of 1185 million reads and identified a total of 199,351 DHSs through ~ 30% unique mapping reads. It should be noted that more than half of DNase-seq reads mapped multiple genome locations and were not analyzed in order to achieve a high specificity of peak profile and to avoid bias from repetitive genomic regions. Distinct chromatin accessibilities were observed in the ovules (0 and 3 DPA) compared to the fiber elongation stages (8, 12, 15, and 18 DPA). Besides, the chromatin accessibility during ovules was particularly elevated in genomic regions enriched with transposable elements (TEs) and genes in TE-enriched regions were involved in ovule cell division. We analyzed cis-regulatory modules and revealed the influence of hormones on fiber development from the regulatory divergence of transcription factor (TF) motifs. Finally, we constructed a reliable regulatory network of TFs related to ovule and fiber development based on chromatin accessibility and gene co-expression network. From this network, we discovered a novel TF, WRKY46, which may shape fiber development by regulating the lignin content. CONCLUSIONS Our results not only reveal the contribution of TEs in fiber development, but also predict and validate the TFs related to fiber development, which will benefit the research of cotton fiber molecular breeding.
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Affiliation(s)
- Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Jingjing Gao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored By Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Shuang Cheng
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Qi You
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Peng Liu
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Pengtao Li
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Shulin Zhang
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Nan Hu
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Shuo Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Qingqing Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Zhaoguo Li
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Guowei Ao
- Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Fang Liu
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Kunbo Wang
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Michigan State University AgBioResearch, East Lansing, MI, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Wenli Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored By Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, 455000, China.
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China.
- Zhengzhou University, Zhengzhou, Henan, 450001, China.
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9
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Smet D, Opdebeeck H, Vandepoele K. Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1212073. [PMID: 37528982 PMCID: PMC10390317 DOI: 10.3389/fpls.2023.1212073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 08/03/2023]
Abstract
Plants have evolved various mechanisms to adapt to adverse environmental stresses, such as the modulation of gene expression. Expression of stress-responsive genes is controlled by specific regulators, including transcription factors (TFs), that bind to sequence-specific binding sites, representing key components of cis-regulatory elements and regulatory networks. Our understanding of the underlying regulatory code remains, however, incomplete. Recent studies have shown that, by training machine learning (ML) algorithms on genomic sequence features, it is possible to predict which genes will transcriptionally respond to a specific stress. By identifying the most important features for gene expression prediction, these trained ML models allow, in theory, to further elucidate the regulatory code underlying the transcriptional response to abiotic stress. Here, we trained random forest ML models to predict gene expression in rice (Oryza sativa) in response to heat or drought stress. Apart from thoroughly assessing model performance and robustness across various input training data, the importance of promoter and gene body sequence features to train ML models was evaluated. The use of enriched promoter oligomers, complementing known TF binding sites, allowed us to gain novel insights in DNA motifs contributing to the stress regulatory code. By comparing genomic feature importance scores for drought and heat stress over time, general and stress-specific genomic features contributing to the performance of the learned models and their temporal variation were identified. This study provides a solid foundation to build and interpret ML models accurately predicting transcriptional responses and enables novel insights in biological sequence features that are important for abiotic stress responses.
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Affiliation(s)
- Dajo Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Helder Opdebeeck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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10
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Hossain NI, Tabassum S. A hybrid multifunctional physicochemical sensor suite for continuous monitoring of crop health. Sci Rep 2023; 13:9848. [PMID: 37330620 PMCID: PMC10276867 DOI: 10.1038/s41598-023-37041-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023] Open
Abstract
This work reports a first-of-its-kind hybrid wearable physicochemical sensor suite that we call PlantFit for simultaneous measurement of two key phytohormones, salicylic acid, and ethylene, along with vapor pressure deficit and radial growth of stem in live plants. The sensors are developed using a low-cost and roll-to-roll screen printing technology. A single integrated flexible patch that contains temperature, humidity, salicylic acid, and ethylene sensors, is installed on the leaves of live plants. The strain sensor with in-built pressure correction capability is wrapped around the plant stem to provide pressure-compensated stem diameter measurements. The sensors provide real-time information on plant health under different amounts of water stress conditions. The sensor suite is installed on bell pepper plants for 40 days and measurements of salicylic acid, ethylene, temperature, humidity, and stem diameter are recorded daily. In addition, sensors are installed on different parts of the same plant to investigate the spatiotemporal dynamics of water transport and phytohormone responses. Subsequent correlation and principal component analyses demonstrate the strong association between hormone levels, vapor pressure deficit, and water transport in the plant. Our findings suggest that the mass deployment of PlantFit in agricultural settings will aid growers in detecting water stress/deficiency early and in implementing early intervention measures to reduce stress-induced yield decline.
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11
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Depuydt T, De Rybel B, Vandepoele K. Charting plant gene functions in the multi-omics and single-cell era. TRENDS IN PLANT SCIENCE 2023; 28:283-296. [PMID: 36307271 DOI: 10.1016/j.tplants.2022.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.
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Affiliation(s)
- Thomas Depuydt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; Vlaams Instituut voor Biotechnologie, Center for Plant Systems Biology, Ghent, Belgium; Ghent University, Bioinformatics Institute Ghent, Ghent, Belgium.
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12
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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13
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Vielba JM, Rico S, Sevgin N, Castro-Camba R, Covelo P, Vidal N, Sánchez C. Transcriptomics Analysis Reveals a Putative Role for Hormone Signaling and MADS-Box Genes in Mature Chestnut Shoots Rooting Recalcitrance. PLANTS (BASEL, SWITZERLAND) 2022; 11:3486. [PMID: 36559597 PMCID: PMC9786281 DOI: 10.3390/plants11243486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Maturation imposes several changes in plants, which are particularly drastic in the case of trees. In recalcitrant woody species, such as chestnut (Castanea sativa Mill.), one of the major maturation-related shifts is the loss of the ability to form adventitious roots in response to auxin treatment as the plant ages. To analyze the molecular mechanisms underlying this phenomenon, an in vitro model system of two different lines of microshoots derived from the same field-grown tree was established. While juvenile-like shoots root readily when treated with exogenous auxin, microshoots established from the crown of the tree rarely form roots. In the present study, a transcriptomic analysis was developed to compare the gene expression patterns in both types of shoots 24 h after hormone and wounding treatment, matching the induction phase of the process. Our results support the hypothesis that the inability of adult chestnut tissues to respond to the inductive treatment relies in a deep change of gene expression imposed by maturation that results in a significant transcriptome modification. Differences in phytohormone signaling seem to be the main cause for the recalcitrant behavior of mature shoots, with abscisic acid and ethylene negatively influencing the rooting ability of the chestnut plants. We have identified a set of related MADS-box genes whose expression is modified but not suppressed by the inductive treatment in mature shoots, suggesting a putative link of their activity with the rooting-recalcitrant behavior of this material. Overall, distinct maturation-derived auxin sensibility and homeostasis, and the related modifications in the balance with other phytohormones, seem to govern the outcome of the process in each type of shoots.
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Affiliation(s)
- Jesús Mª Vielba
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
| | - Saleta Rico
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
| | - Nevzat Sevgin
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
- Department of Horticulture, University of Sirnak, 73100 Sirnak, Turkey
| | - Ricardo Castro-Camba
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
| | - Purificación Covelo
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
| | - Nieves Vidal
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
| | - Conchi Sánchez
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
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14
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Ranaweera T, Brown BN, Wang P, Shiu SH. Temporal regulation of cold transcriptional response in switchgrass. FRONTIERS IN PLANT SCIENCE 2022; 13:998400. [PMID: 36299783 PMCID: PMC9589291 DOI: 10.3389/fpls.2022.998400] [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: 07/19/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis-regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k-mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k-mers, referred to as putative cis-regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies.
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Affiliation(s)
- Thilanka Ranaweera
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Energy (DOE) Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - Brianna N.I. Brown
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Peipei Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Energy (DOE) Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Energy (DOE) Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, United States
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15
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Meuriot F, Prud'homme MP, Noiraud-Romy N. Defoliation, wounding, and methyl jasmonate induce expression of the sucrose lateral transporter LpSUT1 in ryegrass (Lolium perenne L.). PHYSIOLOGIA PLANTARUM 2022; 174:e13744. [PMID: 35780469 DOI: 10.1111/ppl.13744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/21/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Ryegrass (Lolium perenne L.) regrowth after defoliation results from the mobilization of sugar reserves (mainly fructans) and, simultaneously, the efficient lateral transport of sucrose toward growing tissues. However, as for grasses overall, it is not yet known if the induction of this transport is solely linked to the sugar demand of growing tissues via the modification of sugar content at the tissue or cellular level or if it could be triggered by a wounding signal due to the defoliation itself. Ryegrass plants were therefore submitted to total or partial defoliation, pinning of the leaf blades to simulate wounding, or to leaf spraying with 100 μM methyl jasmonate (MeJA), a phytohormone related to wounding. As a response to total or partial defoliation, fructans were mobilized, and the expression of the sucrose lateral transporter LpSUT1 was induced. This highlights an efficient intra-plant compensatory partitioning of sugar resources between defoliated and intact tillers, resulting in the adaptation to regrow after moderate to severe defoliation. The MeJA treatment strongly decreased fructan content. Pinning and especially MeJA largely and quickly increased sucrose content and LpSUT1 transcript levels in leaf sheaths and elongating leaf bases, suggesting a direct effect of wounding on the upregulation of the sucrose lateral transporter. The overall results suggest that sucrose transport capacity and fructan degradation are induced by defoliation through the modification of source-sink relationships for sugars at the plant level and are mediated by phytohormones associated with wounding, such as jasmonates.
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Affiliation(s)
- Frédéric Meuriot
- Normandie Univ, UNICAEN, INRAE, EVA Ecophysiologie Végétale Agronomie et nutritions NCS, Caen, France
| | - Marie-Pascale Prud'homme
- Normandie Univ, UNICAEN, INRAE, EVA Ecophysiologie Végétale Agronomie et nutritions NCS, Caen, France
| | - Nathalie Noiraud-Romy
- Normandie Univ, UNICAEN, INRAE, EVA Ecophysiologie Végétale Agronomie et nutritions NCS, Caen, France
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16
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Arabia A, Munné-Bosch S, Muñoz P. Melatonin triggers tissue-specific changes in anthocyanin and hormonal contents during postharvest decay of Angeleno plums. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111287. [PMID: 35643621 DOI: 10.1016/j.plantsci.2022.111287] [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: 12/27/2021] [Revised: 03/07/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Plum is a stone fruit that stands out for having a short shelf-life because of its high susceptibility to rapid deterioration. Part of this deterioration is explained by fruit overripening. Recently, the role of melatonin in delaying postharvest decay has been investigated but its regulatory function during overripening is still under extensive debate. In this study, to understand physiological events taking place in plums overripening and elucidate the role of melatonin on the postharvest quality of these fruits and its relationship to other plant hormones, Angeleno plums were sprayed with 10-4 M of melatonin solution immediately after harvest. We carried out tissue-specific (mesocarp and exocarp) analysis of total phenols and anthocyanin quantification, as well as the evaluation of different phytohormones by LC-MS/MS and fruit quality parameters. Results showed that during postharvest, endogenous melatonin contents decreased both in the mesocarp and the exocarp of Angeleno plums. Likewise, plum firmness also decreased and a strong correlation was found for this parameter with jasmonic acid (JA) and cytokinins. Conversely, after exogenous melatonin application, endogenous melatonin content increased both in mesocarp and exocarp but it had a differential effect depending on the plum tissue. Indeed, total phenol and anthocyanin contents arose by 21% and 58%, respectively, in the mesocarp after melatonin treatment but no variations were found in the exocarp of Angeleno plums. Hormonal analysis of Angeleno mesocarp also revealed an increase in the JA and its precursor, 12-oxo-phytodienoic acid (OPDA), on the fourth day after melatonin application as well as a positive correlation between melatonin and gibberellin 1 (GA1). These results suggest that melatonin may be acting as a signal molecule increasing phenolic compounds contents through direct regulation and by signaling with other phytohormones. Therefore, this research provides valuable information for understanding the regulatory role of melatonin and its relationship with plant hormones during overripening to contribute to improve the postharvest quality of plums.
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Affiliation(s)
- Alba Arabia
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain; Research Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain; Research Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Paula Muñoz
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain; Research Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain.
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17
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Myers RJ, Fichman Y, Stacey G, Mittler R. Extracellular ATP plays an important role in systemic wound response activation. PLANT PHYSIOLOGY 2022; 189:1314-1325. [PMID: 35348752 PMCID: PMC9237675 DOI: 10.1093/plphys/kiac148] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/06/2022] [Indexed: 06/02/2023]
Abstract
Mechanical wounding occurs in plants during biotic or abiotic stresses and is associated with the activation of long-distance signaling pathways that trigger wound responses in systemic tissues. Among the different systemic signals activated by wounding are electric signals, calcium, hydraulic, and reactive oxygen species (ROS) waves. The release of glutamate (Glu) from cells at the wounded tissues was recently proposed to trigger systemic signal transduction pathways via GLU-LIKE RECEPTORs (GLRs). However, the role of another important compound released from cells during wounding (extracellular ATP [eATP]) in triggering systemic responses is not clear. Here, we show in Arabidopsis (Arabidopsis thaliana) that wounding results in the accumulation of nanomolar levels of eATP and that these levels are sufficient to trigger the systemic ROS wave. We further show that the triggering of the ROS wave by eATP during wounding requires the PURINORECEPTOR 2 KINASE (P2K) receptor. Application of eATP to unwounded leaves triggered the ROS wave, and the activation of the ROS wave by wounding or eATP application was suppressed in mutants deficient in P2Ks (e.g. p2k1-3, p2k2, and p2k1-3p2k2). In addition, expression of systemic wound response (SWR) transcripts was suppressed in mutants deficient in P2Ks during wounding. Interestingly, the effect of Glu and eATP application on ROS wave activation was not additive, suggesting that these two compounds function in the same pathway to trigger the ROS wave. Our findings reveal that in addition to sensing Glu via GLRs, eATP sensed by P2Ks plays a key role in the triggering of SWRs in plants.
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Affiliation(s)
- Ronald J Myers
- The Division of Plant Sciences Technology, Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65201, USA
| | - Yosef Fichman
- The Division of Plant Sciences Technology, Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65201, USA
| | - Gary Stacey
- The Division of Plant Sciences Technology, Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65201, USA
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18
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Herrera-Ubaldo H. Decoding the cis-regulation of tomato fruit development with deep learning. THE PLANT CELL 2022; 34:2108-2109. [PMID: 35325244 PMCID: PMC9134057 DOI: 10.1093/plcell/koac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
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19
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Zeng L, Chen H, Wang Y, Hicks D, Ke H, Pruneda-Paz J, Dehesh K. ORA47 is a transcriptional regulator of a general stress response hub. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:562-571. [PMID: 35092704 DOI: 10.1111/tpj.15688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Transcriptional regulators of the general stress response (GSR) reprogram the expression of selected genes to transduce informational signals into cellular events, ultimately manifested in a plant's ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) binding to the previously established functional GSR motif, termed the rapid stress response element (RSRE). This led to the isolation of octadecanoid-responsive AP2/ERF-domain transcription factor 47 (ORA47), a methyl jasmonate inducible protein. Subsequently, ORA47 transcriptional activity was confirmed using the RSRE-driven luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in the induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of methyl jasmonate led to enhanced levels of ORA47 and CAMTA3 transcripts, as well as the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity. Collectively, the present study provides fresh insight into the initial features of the mechanism that transduces informational signals into adaptive responses. This mechanism involves the functional interplay between the JA biosynthesis/signaling cascade and the transcriptional reprogramming that potentiates GSR. Furthermore, these findings offer a window into the role of intraorganellar communication in the establishment of adaptive responses.
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Affiliation(s)
- Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Hao Chen
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yaqi Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Derrick Hicks
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Haiyan Ke
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Jose Pruneda-Paz
- Section of Cell and Developmental Biology, University of California, La Jolla, CA, 92093, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
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20
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Kenchanmane Raju SK. Machine learning models reveal the importance of time-point specific cis-regulatory elements in Arabidopsis thaliana wounding response. THE PLANT CELL 2022; 34:716-717. [PMID: 35231110 PMCID: PMC8824588 DOI: 10.1093/plcell/koab288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Sunil Kumar Kenchanmane Raju
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
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