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Duan Y, Han M, Schikora A. The coordinated responses of host plants to diverse N-acyl homoserine lactones. PLANT SIGNALING & BEHAVIOR 2024; 19:2356406. [PMID: 38785260 PMCID: PMC11135860 DOI: 10.1080/15592324.2024.2356406] [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: 04/05/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
In nature, co-evolution shaped balanced entities of host plants and their associated microorganism. Plants maintain this balance by detecting their associated microorganism and coordinating responses to them. Quorum sensing (QS) is a widespread bacterial cell-to-cell communication mechanism to modulate the collective behavior of bacteria. As a well-characterized QS signal, N-acyl homoserine lactones (AHL) also influence plant fitness. Plants need to coordinate their responses to diverse AHL molecules since they might host bacteria producing various AHL. This opinion paper discusses plants response to a mixture of multiple AHL molecules. The function of various phytohormones and WRKY transcription factors seems to be characteristic for plants' response to multiple AHL. Additionally, the perspectives and possible approaches to facilitate further research and the application of AHL-producing bacteria are discussed.
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Affiliation(s)
- Yongming Duan
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Min Han
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Adam Schikora
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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2
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Pratx L, Crawford T, Bäurle I. Mechanisms of heat stress-induced transcriptional memory. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102590. [PMID: 38968911 DOI: 10.1016/j.pbi.2024.102590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 07/07/2024]
Abstract
Transcriptional memory allows organisms to store information about transcriptional reprogramming in response to a stimulus. In plants, this often involves the response to an abiotic stress, which in nature may be cyclical or recurring. Such transcriptional memory confers sustained induction or enhanced re-activation in response to a recurrent stimulus, which may increase chances of survival and fitness. Heat stress (HS) has emerged as an excellent model system to study transcriptional memory in plants, and much progress has been made in elucidating the molecular mechanisms underlying this phenomenon. Here, we review how histone turnover and transcriptional co-regulator complexes contribute to reprogramming of transcriptional responses.
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Affiliation(s)
- Loris Pratx
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Tim Crawford
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Isabel Bäurle
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany.
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3
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Yajnik KN, Singh IK, Singh A. lncRNAs and epigenetics regulate plant's resilience against biotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108892. [PMID: 38964086 DOI: 10.1016/j.plaphy.2024.108892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
With the advent of transcriptomic techniques involving single-stranded RNA sequencing and chromatin isolation by RNA purification-based sequencing, transcriptomic studies of coding and non-coding RNAs have been executed efficiently. These studies acknowledged the role of non-coding RNAs in modulating gene expression. Long non-coding RNAs (lncRNAs) are a kind of non-coding RNAs having lengths of >200 nucleotides, playing numerous roles in plant developmental processes such as photomorphogenesis, epigenetic changes, reproductive tissue development, and in regulating biotic and abiotic stresses. Epigenetic changes further control gene expression by changing their state to "ON-OFF" and also regulate stress memory and its transgenerational inheritance. With well-established regulatory mechanisms, they act as guides, scaffolds, signals, and decoys to modulate gene expression. They act as a major operator of post-transcriptional modifications such as histone and epigenetic modifications, and DNA methylations. The review elaborates on the roles of lncRNAs in plant immunity and also discusses how epigenetic markers alter gene expression in response to pest/pathogen attack and influences chromatin-associated stress memory as well as transgenerational inheritance of epigenetic imprints in plants. The review further summarizes some research studies on how histone modifications and DNA methylations resist pathogenic and pest attacks by activating defense-related genes.
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Affiliation(s)
- Kalpesh Nath Yajnik
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India.
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4
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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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5
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Ganie SA, McMulkin N, Devoto A. The role of priming and memory in rice environmental stress adaptation: Current knowledge and perspectives. PLANT, CELL & ENVIRONMENT 2024; 47:1895-1915. [PMID: 38358119 DOI: 10.1111/pce.14855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Plant responses to abiotic stresses are dynamic, following the unpredictable changes of physical environmental parameters such as temperature, water and nutrients. Physiological and phenotypical responses to stress are intercalated by periods of recovery. An earlier stress can be remembered as 'stress memory' to mount a response within a generation or transgenerationally. The 'stress priming' phenomenon allows plants to respond quickly and more robustly to stressors to increase survival, and therefore has significant implications for agriculture. Although evidence for stress memory in various plant species is accumulating, understanding of the mechanisms implicated, especially for crops of agricultural interest, is in its infancy. Rice is a major food crop which is susceptible to abiotic stresses causing constraints on its cultivation and yield globally. Advancing the understanding of the stress response network will thus have a significant impact on rice sustainable production and global food security in the face of climate change. Therefore, this review highlights the effects of priming on rice abiotic stress tolerance and focuses on specific aspects of stress memory, its perpetuation and its regulation at epigenetic, transcriptional, metabolic as well as physiological levels. The open questions and future directions in this exciting research field are also laid out.
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Affiliation(s)
- Showkat Ahmad Ganie
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
| | - Nancy McMulkin
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
| | - Alessandra Devoto
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
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Roychowdhury R, Mishra S, Anand G, Dalal D, Gupta R, Kumar A, Gupta R. Decoding the molecular mechanism underlying salicylic acid (SA)-mediated plant immunity: an integrated overview from its biosynthesis to the mode of action. PHYSIOLOGIA PLANTARUM 2024; 176:e14399. [PMID: 38894599 DOI: 10.1111/ppl.14399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/05/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
Salicylic acid (SA) is an important phytohormone, well-known for its regulatory role in shaping plant immune responses. In recent years, significant progress has been made in unravelling the molecular mechanisms underlying SA biosynthesis, perception, and downstream signalling cascades. Through the concerted efforts employing genetic, biochemical, and omics approaches, our understanding of SA-mediated defence responses has undergone remarkable expansion. In general, following SA biosynthesis through Avr effectors of the pathogens, newly synthesized SA undergoes various biochemical changes to achieve its active/inactive forms (e.g. methyl salicylate). The activated SA subsequently triggers signalling pathways associated with the perception of pathogen-derived signals, expression of defence genes, and induction of systemic acquired resistance (SAR) to tailor the intricate regulatory networks that coordinate plant immune responses. Nonetheless, the mechanistic understanding of SA-mediated plant immune regulation is currently limited because of its crosstalk with other signalling networks, which makes understanding this hormone signalling more challenging. This comprehensive review aims to provide an integrated overview of SA-mediated plant immunity, deriving current knowledge from diverse research outcomes. Through the integration of case studies, experimental evidence, and emerging trends, this review offers insights into the regulatory mechanisms governing SA-mediated immunity and signalling. Additionally, this review discusses the potential applications of SA-mediated defence strategies in crop improvement, disease management, and sustainable agricultural practices.
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Affiliation(s)
- Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - Volcani Institute, Rishon Lezion, Israel
| | - Sapna Mishra
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - Volcani Institute, Rishon Lezion, Israel
| | - Gautam Anand
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - Volcani Institute, Rishon Lezion, Israel
| | - Debalika Dalal
- Department of Botany, Visva-Bharati Central University, Santiniketan, West Bengal, India
| | - Rupali Gupta
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - Volcani Institute, Rishon Lezion, Israel
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, South Korea
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Valencia-Lozano E, Cabrera-Ponce JL, Barraza A, López-Calleja AC, García-Vázquez E, Rivera-Toro DM, de Folter S, Alvarez-Venegas R. Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom. PLoS One 2024; 19:e0301169. [PMID: 38557903 PMCID: PMC10984418 DOI: 10.1371/journal.pone.0301169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
At present, the development of plants with improved traits like superior quality, high yield, or stress resistance, are highly desirable in agriculture. Accelerated crop improvement, however, must capitalize on revolutionary new plant breeding technologies, like genetically modified and gene-edited crops, to heighten food crop traits. Genome editing still faces ineffective methods for the transformation and regeneration of different plant species and must surpass the genotype dependency of the transformation process. Tomato is considered an alternative plant model system to rice and Arabidopsis, and a model organism for fleshy-fruited plants. Furthermore, tomato cultivars like Micro-Tom are excellent models for tomato research due to its short life cycle, small size, and capacity to grow at high density. Therefore, we developed an indirect somatic embryo protocol from cotyledonary tomato explants and used this to generate epigenetically edited tomato plants for the SlWRKY29 gene via CRISPR-activation (CRISPRa). We found that epigenetic reprogramming for SlWRKY29 establishes a transcriptionally permissive chromatin state, as determined by an enrichment of the H3K4me3 mark. A whole transcriptome analysis of CRISPRa-edited pro-embryogenic masses and mature somatic embryos allowed us to characterize the mechanism driving somatic embryo induction in the edited tomato cv. Micro-Tom. Furthermore, we show that enhanced embryo induction and maturation are influenced by the transcriptional effector employed during CRISPRa, as well as by the medium composition and in vitro environmental conditions such as osmotic components, plant growth regulators, and light intensity.
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Affiliation(s)
- Eliana Valencia-Lozano
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Unidad Irapuato, Irapuato, Guanajuato, México
| | - José Luis Cabrera-Ponce
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Unidad Irapuato, Irapuato, Guanajuato, México
| | - Aarón Barraza
- Programa de Agricultura en Zonas Áridas, CONACYT-CIBNOR, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - Alberto Cristian López-Calleja
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Unidad Irapuato, Irapuato, Guanajuato, México
| | - Elsa García-Vázquez
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Unidad Irapuato, Irapuato, Guanajuato, México
| | - Diana Marcela Rivera-Toro
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Unidad Irapuato, Irapuato, Guanajuato, México
| | - Stefan de Folter
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Unidad de Genómica Avanzada, Irapuato, Guanajuato, México
| | - Raúl Alvarez-Venegas
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Unidad Irapuato, Irapuato, Guanajuato, México
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Nabi Z, Manzoor S, Nabi SU, Wani TA, Gulzar H, Farooq M, Arya VM, Baloch FS, Vlădulescu C, Popescu SM, Mansoor S. Pattern-Triggered Immunity and Effector-Triggered Immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:587-604. [PMID: 38737322 PMCID: PMC11087456 DOI: 10.1007/s12298-024-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024]
Abstract
The elucidation of the molecular basis underlying plant-pathogen interactions is imperative for the development of sustainable resistance strategies against pathogens. Plants employ a dual-layered immunological detection and response system wherein cell surface-localized Pattern Recognition Receptors (PRRs) and intracellular Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs) play pivotal roles in initiating downstream signalling cascades in response to pathogen-derived chemicals. Pattern-Triggered Immunity (PTI) is associated with PRRs and is activated by the recognition of conserved molecular structures, known as Pathogen-Associated Molecular Patterns. When PTI proves ineffective due to pathogenic effectors, Effector-Triggered Immunity (ETI) frequently confers resistance. In ETI, host plants utilize NLRs to detect pathogen effectors directly or indirectly, prompting a rapid and more robust defense response. Additionally epigenetic mechanisms are participating in plant immune memory. Recently developed technologies like CRISPR/Cas9 helps in exposing novel prospects in plant pathogen interactions. In this review we explore the fascinating crosstalk and cooperation between PRRs and NLRs. We discuss epigenomic processes and CRISPR/Cas9 regulating immune response in plants and recent findings that shed light on the coordination of these defense layers. Furthermore, we also have discussed the intricate interactions between the salicylic acid and jasmonic acid signalling pathways in plants, offering insights into potential synergistic interactions that would be harnessed for the development of novel and sustainable resistance strategies against diverse group of pathogens.
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Affiliation(s)
- Zarka Nabi
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132 India
| | | | - Humira Gulzar
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Mehreena Farooq
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025 India
| | - Vivak M. Arya
- Division of Soil Science and Agriculture Chemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin Turkey
| | - Carmen Vlădulescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju, 63243 Republic of Korea
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9
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Nishio H, Kawakatsu T, Yamaguchi N. Beyond heat waves: Unlocking epigenetic heat stress memory in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:1934-1951. [PMID: 37878744 DOI: 10.1093/plphys/kiad558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
Plants remember their exposure to environmental changes and respond more effectively the next time they encounter a similar change by flexibly altering gene expression. Epigenetic mechanisms play a crucial role in establishing such memory of environmental changes and fine-tuning gene expression. With the recent advancements in biochemistry and sequencing technologies, it has become possible to characterize the dynamics of epigenetic changes on scales ranging from short term (minutes) to long term (generations). Here, our main focus is on describing the current understanding of the temporal regulation of histone modifications and chromatin changes during exposure to short-term recurring high temperatures and reevaluating them in the context of natural environments. Investigations of the dynamics of histone modifications and chromatin structural changes in Arabidopsis after repeated exposure to heat at short intervals have revealed the detailed molecular mechanisms of short-term heat stress memory, which include histone modification enzymes, chromatin remodelers, and key transcription factors. In addition, we summarize the spatial regulation of heat responses. Based on the natural temperature patterns during summer, we discuss how plants cope with recurring heat stress occurring at various time intervals by utilizing 2 distinct types of heat stress memory mechanisms. We also explore future research directions to provide a more precise understanding of the epigenetic regulation of heat stress memory.
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Affiliation(s)
- Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga 522-8522, Japan
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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Mierziak J, Wojtasik W. Epigenetic weapons of plants against fungal pathogens. BMC PLANT BIOLOGY 2024; 24:175. [PMID: 38443788 PMCID: PMC10916060 DOI: 10.1186/s12870-024-04829-8] [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: 07/14/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant's response to various biotic stresses relies heavily on its ability to rapidly adjust the transcriptome. External signals are transmitted to the nucleus, leading to activation of transcription factors that subsequently enhance the expression of specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which are closely linked to chromatin states, regulate gene expression associated with defense against biotic stress. Additionally, chromatin remodelers and non-coding RNA play a significant role in plant defense against stressors. These molecular modifications enable plants to exhibit enhanced resistance and productivity under diverse environmental conditions. Epigenetic mechanisms also contribute to stress-induced environmental epigenetic memory and priming in plants, enabling them to recall past molecular experiences and utilize this stored information for adaptation to new conditions. In the arms race between fungi and plants, a significant aspect is the cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi utilize sRNA as an effector molecule to silence plant resistance genes, while plants transport sRNA, primarily through extracellular vesicles, to pathogens in order to suppress virulence-related genes. In this review, we summarize contemporary knowledge on epigenetic mechanisms of plant defense against attack by pathogenic fungi. The role of epigenetic mechanisms during plant-fungus symbiotic interactions is also considered.
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Affiliation(s)
- Justyna Mierziak
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland
| | - Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland.
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11
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Corrêa RL, Kutnjak D, Ambrós S, Bustos M, Elena SF. Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance. BMC PLANT BIOLOGY 2024; 24:172. [PMID: 38443837 PMCID: PMC10913459 DOI: 10.1186/s12870-024-04866-3] [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: 07/04/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Plant responses to a wide range of stresses are known to be regulated by epigenetic mechanisms. Pathogen-related investigations, particularly against RNA viruses, are however scarce. It has been demonstrated that Arabidopsis thaliana plants defective in some members of the RNA-directed DNA methylation (RdDM) or histone modification pathways presented differential susceptibility to the turnip mosaic virus. In order to identify genes directly targeted by the RdDM-related RNA Polymerase V (POLV) complex and the histone demethylase protein JUMONJI14 (JMJ14) during infection, the transcriptomes of infected mutant and control plants were obtained and integrated with available chromatin occupancy data for various epigenetic proteins and marks. RESULTS A comprehensive list of virus-responsive gene candidates to be regulated by the two proteins was obtained. Twelve genes were selected for further characterization, confirming their dynamic regulation during the course of infection. Several epigenetic marks on their promoter sequences were found using in silico data, raising confidence that the identified genes are actually regulated by epigenetic mechanisms. The altered expression of six of these genes in mutants of the methyltransferase gene CURLY LEAF and the histone deacetylase gene HISTONE DEACETYLASE 19 suggests that some virus-responsive genes may be regulated by multiple coordinated epigenetic complexes. A temporally separated multiple plant virus infection experiment in which plants were transiently infected with one virus and then infected by a second one was designed to investigate the possible roles of the identified POLV- and JMJ14-regulated genes in wild-type (WT) plants. Plants that had previously been stimulated with viruses were found to be more resistant to subsequent virus challenge than control plants. Several POLV- and JMJ14-regulated genes were found to be regulated in virus induced resistance in WT plants, with some of them poisoned to be expressed in early infection stages. CONCLUSIONS A set of confident candidate genes directly regulated by the POLV and JMJ14 proteins during virus infection was identified, with indications that some of them may be regulated by multiple epigenetic modules. A subset of these genes may also play a role in the tolerance of WT plants to repeated, intermittent virus infections.
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Affiliation(s)
- Régis L Corrêa
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain.
- Department of Genetics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-590, Brazil.
| | - Denis Kutnjak
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Silvia Ambrós
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
| | - Mónica Bustos
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
| | - Santiago F Elena
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
- The Santa Fe Institute, Santa Fe, NM, 87501, USA
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12
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Kashyap S, Agarwala N, Sunkar R. Understanding plant stress memory traits can provide a way for sustainable agriculture. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111954. [PMID: 38092267 DOI: 10.1016/j.plantsci.2023.111954] [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: 07/26/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/01/2024]
Abstract
Being sessile, plants encounter various biotic and abiotic threats in their life cycle. To minimize the damages caused by such threats, plants have acquired sophisticated response mechanisms. One major such response includes memorizing the encountered stimuli in the form of a metabolite, hormone, protein, or epigenetic marks. All of these individually as well as together, facilitate effective transcriptional and post-transcriptional responses upon encountering the stress episode for a second time during the life cycle and in some instances even in the future generations. This review attempts to highlight the recent advances in the area of plant memory. A detailed understanding of plant memory has the potential to offer solutions for developing climate-resilient crops for sustainable agriculture.
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Affiliation(s)
- Sampurna Kashyap
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India.
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
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Venios X, Gkizi D, Nisiotou A, Korkas E, Tjamos SE, Zamioudis C, Banilas G. Emerging Roles of Epigenetics in Grapevine and Winegrowing. PLANTS (BASEL, SWITZERLAND) 2024; 13:515. [PMID: 38498480 PMCID: PMC10893341 DOI: 10.3390/plants13040515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype-environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.
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Affiliation(s)
- Xenophon Venios
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
| | - Danai Gkizi
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
| | - Aspasia Nisiotou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “Demeter”, Sofokli Venizelou 1, 14123 Lykovryssi, Greece;
| | - Elias Korkas
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
| | - Sotirios E. Tjamos
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece;
| | - Christos Zamioudis
- Department of Agricultural Development, Democritus University of Thrace, Pantazidou 193, 68200 Orestiada, Greece;
| | - Georgios Banilas
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
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Sistenich AJ, Fürtauer L, Scheele F, Conrath U. Marker and readout genes for defense priming in Pseudomonas cannabina pv. alisalensis interaction aid understanding systemic immunity in Arabidopsis. Sci Rep 2024; 14:3489. [PMID: 38347062 PMCID: PMC10861594 DOI: 10.1038/s41598-024-53982-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
Following localized infection, the entire plant foliage becomes primed for enhanced defense. However, specific genes induced during defense priming (priming-marker genes) and those showing increased expression in defense-primed plants upon rechallenge (priming-readout genes) remain largely unknown. In our Arabidopsis thaliana study, genes AT1G76960 (function unknown), CAX3 (encoding a vacuolar Ca2+/H+ antiporter), and CRK4 (encoding a cysteine-rich receptor-like protein kinase) were strongly expressed during Pseudomonas cannabina pv. alisalensis-induced defense priming, uniquely marking the primed state for enhanced defense. Conversely, PR1 (encoding a pathogenesis-related protein), RLP23 and RLP41 (both encoding receptor-like proteins) were similarly activated in defense-primed plants before and after rechallenge, suggesting they are additional marker genes for defense priming. In contrast, CASPL4D1 (encoding Casparian strip domain-like protein 4D1), FRK1 (encoding flg22-induced receptor-like kinase), and AT3G28510 (encoding a P loop-containing nucleoside triphosphate hydrolases superfamily protein) showed minimal activation in uninfected, defense-primed, or rechallenged plants, but intensified in defense-primed plants after rechallenge. Notably, mutation in only priming-readout gene NHL25 (encoding NDR1/HIN1-like protein 25) impaired both defense priming and systemic acquired resistance, highlighting its previously undiscovered pivotal role in systemic plant immunity.
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Affiliation(s)
- Andrea J Sistenich
- Plant Biochemistry and Molecular Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany
| | - Lisa Fürtauer
- Plant Molecular Systems Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany
| | - Franziska Scheele
- Plant Biochemistry and Molecular Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany
| | - Uwe Conrath
- Plant Biochemistry and Molecular Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany.
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Siddique AB, Parveen S, Rahman MZ, Rahman J. Revisiting plant stress memory: mechanisms and contribution to stress adaptation. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:349-367. [PMID: 38623161 PMCID: PMC11016036 DOI: 10.1007/s12298-024-01422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/04/2024] [Accepted: 02/22/2024] [Indexed: 04/17/2024]
Abstract
Highly repetitive adverse environmental conditions are encountered by plants multiple times during their lifecycle. These repetitive encounters with stresses provide plants an opportunity to remember and recall the experiences of past stress-associated responses, resulting in better adaptation towards those stresses. In general, this phenomenon is known as plant stress memory. According to our current understanding, epigenetic mechanisms play a major role in plants stress memory through DNA methylation, histone, and chromatin remodeling, and modulating non-coding RNAs. In addition, transcriptional, hormonal, and metabolic-based regulations of stress memory establishment also exist for various biotic and abiotic stresses. Plant memory can also be generated by priming the plants using various stressors that improve plants' tolerance towards unfavorable conditions. Additionally, the application of priming agents has been demonstrated to successfully establish stress memory. However, the interconnection of all aspects of the underlying mechanisms of plant stress memory is not yet fully understood, which limits their proper utilization to improve the stress adaptations in plants. This review summarizes the recent understanding of plant stress memory and its potential applications in improving plant tolerance towards biotic and abiotic stresses.
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Affiliation(s)
- Abu Bakar Siddique
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS 7250 Australia
| | - Sumaya Parveen
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, 1207 Bangladesh
| | - Md Zahidur Rahman
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, 1207 Bangladesh
| | - Jamilur Rahman
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, 1207 Bangladesh
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16
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Crawford T, Siebler L, Sulkowska A, Nowack B, Jiang L, Pan Y, Lämke J, Kappel C, Bäurle I. The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis. EMBO J 2024; 43:437-461. [PMID: 38228917 PMCID: PMC10897291 DOI: 10.1038/s44318-023-00024-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Plants are often exposed to recurring adverse environmental conditions in the wild. Acclimation to high temperatures entails transcriptional responses, which prime plants to better withstand subsequent stress events. Heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurrence of heat stress. Here, we identified CDK8 and MED12, two subunits of the kinase module of the transcription co-regulator complex, Mediator, as promoters of heat stress memory and associated histone modifications in Arabidopsis. CDK8 is recruited to heat-stress memory genes by HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2). Like HSFA2, CDK8 is largely dispensable for the initial gene induction upon HS, and its function in transcriptional memory is thus independent of primary gene activation. In addition to the promoter and transcriptional start region of target genes, CDK8 also binds their 3'-region, where it may promote elongation, termination, or rapid re-initiation of RNA polymerase II (Pol II) complexes during transcriptional memory bursts. Our work presents a complex role for the Mediator kinase module during transcriptional memory in multicellular eukaryotes, through interactions with transcription factors, chromatin modifications, and promotion of Pol II efficiency.
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Affiliation(s)
- Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Lara Siebler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bryan Nowack
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Yufeng Pan
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Srivastava S, Tyagi R, Sharma S. Seed biopriming as a promising approach for stress tolerance and enhancement of crop productivity: a review. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:1244-1257. [PMID: 37824780 DOI: 10.1002/jsfa.13048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/04/2023] [Accepted: 10/13/2023] [Indexed: 10/14/2023]
Abstract
Chemicals are used extensively in agriculture to increase crop production to meet the nutritional needs of an expanding world population. However, their injudicious application adversely affects the soil's physical, chemical and biological properties, subsequently posing a substantial threat to human health and global food security. Beneficial microorganisms improve plant health and productivity with minimal impact on the environment; however, their efficacy greatly relies on the application technique. Biopriming is an advantageous technique that involves the treatment of seeds with beneficial biological agents. It exhibits immense potential in improving the physiological functioning of seeds, thereby playing a pivotal role in their uniform germination and vigor. Biopriming-mediated molecular and metabolic reprogramming imparts stress tolerance to plants, improves plant health, and enhances crop productivity. Furthermore, it is also associated with rehabilitating degraded land, and improving soil fertility, health and nutrient cycling. Although biopriming has vast applications in the agricultural system, its commercialization and utilization by farmers is still in its infancy. This review aims to critically analyze the recent studies based on biopriming-mediated stress mitigation by alteration in physiological, metabolic and molecular processes in plants. Additionally, considering the necessity of popularizing this technique, the major challenges and prospects linked to the commercialization and utilization of this technique in agricultural systems have also been discussed. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Sonal Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Rashi Tyagi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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18
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Zheng Y, Liu Q, Shi S, Zhu X, Chen Y, Lin S, Tian H, Huang L, Wei H. Nitrogen Deficiency Enhances Eggplant Defense against Western Flower Thrips via the Induction of the Jasmonate Pathway. PLANTS (BASEL, SWITZERLAND) 2024; 13:273. [PMID: 38256826 PMCID: PMC10820576 DOI: 10.3390/plants13020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 01/13/2024] [Indexed: 01/24/2024]
Abstract
Plant nutrition is connected to defense against insect herbivores, but the exact mechanism underlying the effect of the nitrogen (N) supply on the anti-herbivore capacity of eggplants (Solanum melongena) has not been studied in detail. Therefore, we examined the impact of low (LN, 0.5 mM) and high (HN, 5 mM) nitrate levels on eggplant resistance against the western flower thrips Frankliniella occidentalis (WFT), a major destructive eggplant pest. Our results showed that LN plants displayed enhanced defense responses to WFT compared to HN plants. This included increased transcript levels of key genes in the jasmonic acid (JA) pathway, the accumulation of JA-amido conjugates (jasmonoyl-isoleucine, jasmonoyl-phenylalanine, and jasmonoyl-valine), JA precursor (12-oxophytodienoic acid), and methyl jasmonate, higher transcript levels of defense marker genes (MPK3, MPK7, and WRKY53), and increased activities of polyphenol oxidase and peroxidase upon a WFT attack. Our findings suggest that N deficiency can prime JA-mediated defense responses in eggplants, resulting in increased anti-herbivore resistance.
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Affiliation(s)
- Yueqin Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Qianxia Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
| | - Shuang Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
| | - Xiaowen Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Shuo Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Houjun Tian
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
| | - Lanyan Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
| | - Hui Wei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (Q.L.); (S.S.); (X.Z.); (Y.C.); (S.L.); (H.T.); (L.H.)
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of the Ministry of Agriculture, Fuzhou 350013, China
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Tian Z, Li K, Sun Y, Chen B, Pan Z, Wang Z, Pang B, He S, Miao Y, Du X. Physiological and transcriptional analyses reveal formation of memory under recurring drought stresses in seedlings of cotton (Gossypium hirsutum). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111920. [PMID: 37944705 DOI: 10.1016/j.plantsci.2023.111920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/03/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Plants are frequently subjected to a range of environmental stresses, including drought, salinity, cold, pathogens, and herbivore attacks. To survive in such conditions, plants have evolved a novel adaptive mechanism known as 'stress memory'. The formation of stress memories necessitates coordinated responses at the cellular, genetic/genomic, and epigenetic levels, involving altered physiological responses, gene activation, hyper-induction and chromatin modification. Cotton (Gossypium spp.) is an important economic crop with numerous applications and high economic value. In this study, we establish G. hirsutum drought memory following cycles of mild drought and re-watering treatments and analyzed memory gene expression patterns. Our findings reveal the physiological, biochemical, and molecular mechanisms underlying drought stress memory formation in G. hirsutum. Specifically, H3K4me3, a histone modification, plays a crucial role in regulating [+ /+ ] transcriptional memory. Moreover, we investigated the intergenerational inheritance of drought stress memory in G. hirsutum. Collectively, our data provides theoretical guidance for cotton breeding.
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Affiliation(s)
- Zailong Tian
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Kun Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China
| | - Yaru Sun
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China
| | - Baojun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhaoe Pan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhenzhen Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Baoyin Pang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shoupu He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China.
| | - Xiongming Du
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China.
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20
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Pratx L, Wendering P, Kappel C, Nikoloski Z, Bäurle I. Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants. EMBO J 2023; 42:e113595. [PMID: 37937667 PMCID: PMC10711655 DOI: 10.15252/embj.2023113595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
Plants often experience recurrent stressful events, for example, during heat waves. They can be primed by heat stress (HS) to improve the survival of more severe heat stress conditions. At certain genes, sustained expression is induced for several days beyond the initial heat stress. This transcriptional memory is associated with hyper-methylation of histone H3 lysine 4 (H3K4me3), but it is unclear how this is maintained for extended periods. Here, we determined histone turnover by measuring the chromatin association of HS-induced histone H3.3. Genome-wide histone turnover was not homogenous; in particular, H3.3 was retained longer at heat stress memory genes compared to HS-induced non-memory genes during the memory phase. While low nucleosome turnover retained H3K4 methylation, methylation loss did not affect turnover, suggesting that low nucleosome turnover sustains H3K4 methylation, but not vice versa. Together, our results unveil the modulation of histone turnover as a mechanism to retain environmentally mediated epigenetic modifications.
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Affiliation(s)
- Loris Pratx
- Plant Epigenetics, Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Philipp Wendering
- Bioinformatics, Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Systems Biology and Mathematical Modeling GroupMax Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Christian Kappel
- Genetics, Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Zoran Nikoloski
- Bioinformatics, Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Systems Biology and Mathematical Modeling GroupMax Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Isabel Bäurle
- Plant Epigenetics, Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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Liu W, Thapa P, Park SW. RD29A and RD29B rearrange genetic and epigenetic markers in priming systemic defense responses against drought and salinity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111895. [PMID: 37838156 DOI: 10.1016/j.plantsci.2023.111895] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/18/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Drought has become the most important limiting factor to crop productions. Research thus far has been devoted to identifying drought-responsive genes (DRGs) via breeding and engineering approaches. Still, these efforts have not resulted in a solution to combat drought's effects because the ectopic expression of most DRGs causes adverse effects that reduce plant growth and yields. Lately, we discovered that two DRGs, Response to Desiccation (RD)29A and RD29B, induced by Paenibacillus polymyxa CR1, a plant growth-promoting rhizobacterium capable of priming drought tolerance and concurrently stimulating plant growth, play pivotal roles in defense responses against drought. In this study, we employ the ChlP and qRT-PCR analyses and further clarify that P. polymyxa CR1 reformats the chromatin/transcriptional memory of RD29s, positioned as upstream controllers that fine-tune the temporal dynamic of stress-regulating transcription factors (TFs) in elaborating induced systemic drought tolerance without growth penalties. Two genes coordinate the upregulation of NAC TFs, while feedback inhibiting CBF TFs, which regulate downstream DRG expressions. This supports that RD29s are unique, feasible transgene candidates for improving plants' survival capacity in both optimal and drought conditions. However, the mode of action of RD29A and RD29B are partly independent, exerting distinct roles in disparate ecological states. When subjected to increasing NaCl concentrations, the KO mutant of RD29A (rd29a) displayed enhanced tolerance compared to WT and rd29b plants, proposing that RD29B, but not RD29A, a key player in conferring WT-like tolerance to salinity stress; further studies will be needed to optimize/maximize their applications in engineering for-profit drought and/or broad-spectrum stress tolerant crops.
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Affiliation(s)
- Wenshan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Parbati Thapa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Sang-Wook Park
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA.
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22
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Saha B, Nayak J, Srivastava R, Samal S, Kumar D, Chanwala J, Dey N, Giri MK. Unraveling the involvement of WRKY TFs in regulating plant disease defense signaling. PLANTA 2023; 259:7. [PMID: 38012461 DOI: 10.1007/s00425-023-04269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 11/29/2023]
Abstract
MAIN CONCLUSION This review article explores the intricate role, regulation, and signaling mechanisms of WRKY TFs in response to biotic stress, particularly emphasizing their pivotal role in the trophism of plant-pathogen interactions. Transcription factors (TFs) play a vital role in governing both plant defense and development by controlling the expression of various downstream target genes. Early studies have shown the differential expression of certain WRKY transcription factors by microbial infections. Several transcriptome-wide studies later demonstrated that diverse sets of WRKYs are significantly activated in the early stages of viral, bacterial, and fungal infections. Furthermore, functional investigations indicated that overexpression or silencing of certain WRKY genes in plants can drastically alter disease symptoms as well as pathogen multiplication rates. Hence the new aspects of pathogen-triggered WRKY TFs mediated regulation of plant defense can be explored. The already recognized roles of WRKYs include transcriptional regulation of defense-related genes, modulation of hormonal signaling, and participation in signal transduction pathways. Some WRKYs have been shown to directly bind to pathogen effectors, acting as decoys or resistance proteins. Notably, the signaling molecules like salicylic acid, jasmonic acid, and ethylene which are associated with plant defense significantly increase the expression of several WRKYs. Moreover, induction of WRKY genes or heightened WRKY activities is also observed during ISR triggered by the beneficial microbes which protect the plants from subsequent pathogen infection. To understand the contribution of WRKY TFs towards disease resistance and their exact metabolic functions in infected plants, further studies are required. This review article explores the intrinsic transcriptional regulation, signaling mechanisms, and hormonal crosstalk governed by WRKY TFs in plant disease defense response, particularly emphasizing their specific role against different biotrophic, hemibiotrophic, and necrotrophic pathogen infections.
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Affiliation(s)
- Baisista Saha
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, Odisha, 751024, India
| | - Jagatjeet Nayak
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, Odisha, 751024, India
| | - Richa Srivastava
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, UP, India
| | - Swarnmala Samal
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, UP, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, UP, India
| | - Jeky Chanwala
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Nrisingha Dey
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Mrunmay Kumar Giri
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, Odisha, 751024, India.
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23
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Harris CJ, Amtmann A, Ton J. Epigenetic processes in plant stress priming: Open questions and new approaches. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102432. [PMID: 37523900 DOI: 10.1016/j.pbi.2023.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 08/02/2023]
Abstract
Priming reflects the capacity of plants to memorise environmental stress experience and improve their response to recurring stress. Epigenetic modifications in DNA and associated histone proteins may carry short-term and long-term memory in the same plant or mediate transgenerational effects, but the evidence is still largely circumstantial. New experimental tools now enable scientists to perform targeted manipulations that either prevent or generate a particular epigenetic modification in a particular location of the genome. Such 'reverse epigenetics' approaches allow for the interrogation of causality between individual priming-induced modifications and their role for altering gene expression and plant performance under recurring stress. Furthermore, combining site-directed epigenetic manipulation with conditional and cell-type specific promoters creates novel opportunities to test and engineer spatiotemporal patterns of priming.
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Affiliation(s)
- C Jake Harris
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Anna Amtmann
- School of Molecular Biosciences, University of Glasgow, Glasgow, G128QQ, UK.
| | - Jurriaan Ton
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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24
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Prusky D, Romanazzi G. Induced Resistance in Fruit and Vegetables: A Host Physiological Response Limiting Postharvest Disease Development. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:279-300. [PMID: 37201920 DOI: 10.1146/annurev-phyto-021722-035135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Harvested fruit and vegetables are perishable, subject to desiccation, show increased respiration during ripening, and are colonized by postharvest fungal pathogens. Induced resistance is a strategy to control diseases by eliciting biochemical processes in fruits and vegetables. This is accomplished by modulating the progress of ripening and senescence, which maintains the produce in a state of heightened resistance to decay-causing fungi. Utilization of induced resistance to protect produce has been improved by scientific tools that better characterize physiological changes in plants. Induced resistance slows the decline of innate immunity after harvest and increases the production of defensive responses that directly inhibit plant pathogens. This increase in defense response in fruits and vegetables contributes to higher amounts of phenols and antioxidant compounds, improving both the quality and appearance of the produce. This review summarizes mechanisms and treatments that induce resistance in harvested fruits and vegetables to suppress fungal colonization. Moreover, it highlights the importance of host maturity and stage of ripening as limiting conditions for the improved expression of induced-resistance processes.
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Affiliation(s)
- Dov Prusky
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel;
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy;
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25
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Badmi R, Prestwich BD. Linker H1 is an 'epi'centre of plant defence. Trends Genet 2023; 39:644-645. [PMID: 37419697 DOI: 10.1016/j.tig.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/09/2023]
Abstract
The role of linker H1 histones in plant defence has recently been investigated. Sheikh et al. found that Arabidopsis thaliana plants that were lacking all three H1 proteins showed increased disease resistance, but when primed, failed to induce enhanced resistance. Differences in epigenetic patterns could be the cause of defective priming.
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Affiliation(s)
- Raghuram Badmi
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland.
| | - Barbara Doyle Prestwich
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
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26
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Wilson SK, Pretorius T, Naidoo S. Mechanisms of systemic resistance to pathogen infection in plants and their potential application in forestry. BMC PLANT BIOLOGY 2023; 23:404. [PMID: 37620815 PMCID: PMC10463331 DOI: 10.1186/s12870-023-04391-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND The complex systemic responses of tree species to fight pathogen infection necessitate attention due to the potential for yield protection in forestry. RESULTS In this paper, both the localized and systemic responses of model plants, such as Arabidopsis and tobacco, are reviewed. These responses were compared to information available that investigates similar responses in woody plant species and their key differences were highlighted. In addition, tree-specific responses that have been documented were summarised, with the critical responses still relying on certain systemic acquired resistance pathways. Importantly, coniferous species have been shown to utilise phenolic compounds in their immune responses. Here we also highlight the lack of focus on systemic induced susceptibility in trees, which can be important to forest health. CONCLUSIONS This review highlights the possible mechanisms of systemic response to infection in woody plant species, their potential applications, and where research may be best focused in future.
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Affiliation(s)
- S K Wilson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - T Pretorius
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - S Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa.
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27
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Furci L, Pascual‐Pardo D, Tirot L, Zhang P, Hannan Parker A, Ton J. Heritable induced resistance in Arabidopsis thaliana: Tips and tools to improve effect size and reproducibility. PLANT DIRECT 2023; 7:e523. [PMID: 37638230 PMCID: PMC10457550 DOI: 10.1002/pld3.523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/18/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023]
Abstract
Over a decade ago, three independent studies reported that pathogen- and herbivore-exposed Arabidopsis thaliana produces primed progeny with increased resistance. Since then, heritable induced resistance (h-IR) has been reported across numerous plant-biotic interactions, revealing a regulatory function of DNA (de)methylation dynamics. However, the identity of the epi-alleles controlling h-IR and the mechanisms by which they prime defense genes remain unknown, while the evolutionary significance of the response requires confirmation. Progress has been hampered by the relatively high variability, low effect size, and sometimes poor reproducibility of h-IR, as is exemplified by a recent study that failed to reproduce h-IR in A. thaliana by Pseudomonas syringae pv. tomato (Pst). This study aimed to improve h-IR effect size and reproducibility in the A. thaliana-Pst interaction. We show that recurrent Pst inoculations of seedlings result in stronger h-IR than repeated inoculations of older plants and that disease-related growth repression in the parents is a reliable marker for h-IR effect size in F1 progeny. Furthermore, RT-qPCR-based expression profiling of genes controlling DNA methylation maintenance revealed that the elicitation of strong h-IR upon seedling inoculations is marked by reduced expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) gene, which is maintained in the apical meristem and transmitted to F1 progeny. Two additional genes, MET1 and CHROMOMETHYLASE3 (CMT3), displayed similar transcriptional repression in progeny from seedling-inoculated plants. Thus, reduced expression of DDM1, MET1, and CMT3 can serve as a marker of robust h-IR in F1 progeny. Our report offers valuable information and markers to improve the effect size and reproducibility of h-IR in the A. thaliana-Pst model interaction.
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Affiliation(s)
- L. Furci
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable FoodThe University of SheffieldSheffieldUK
- Plant Epigenetics UnitOkinawa Institute of Science and TechnologyOnnaOkinawaJapan
| | - D. Pascual‐Pardo
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable FoodThe University of SheffieldSheffieldUK
| | - L. Tirot
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable FoodThe University of SheffieldSheffieldUK
| | - P. Zhang
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable FoodThe University of SheffieldSheffieldUK
| | - A. Hannan Parker
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable FoodThe University of SheffieldSheffieldUK
| | - J. Ton
- Plants, Photosynthesis and Soil, School of Biosciences, Institute for Sustainable FoodThe University of SheffieldSheffieldUK
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28
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Xie SS, Duan CG. Epigenetic regulation of plant immunity: from chromatin codes to plant disease resistance. ABIOTECH 2023; 4:124-139. [PMID: 37581024 PMCID: PMC10423193 DOI: 10.1007/s42994-023-00101-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 08/16/2023]
Abstract
Facing a deteriorating natural environment and an increasing serious food crisis, bioengineering-based breeding is increasing in importance. To defend against pathogen infection, plants have evolved multiple defense mechanisms, including pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). A complex regulatory network acts downstream of these PTI and ETI pathways, including hormone signal transduction and transcriptional reprogramming. In recent years, increasing lines of evidence show that epigenetic factors act, as key regulators involved in the transcriptional reprogramming, to modulate plant immune responses. Here, we summarize current progress on the regulatory mechanism of DNA methylation and histone modifications in plant defense responses. In addition, we also discuss the application of epigenetic mechanism-based resistance strategies in plant disease breeding.
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Affiliation(s)
- Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
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29
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Kappel C, Friedrich T, Oberkofler V, Jiang L, Crawford T, Lenhard M, Bäurle I. Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis. Genome Biol 2023; 24:129. [PMID: 37254211 DOI: 10.1186/s13059-023-02970-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. RESULTS HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. CONCLUSIONS Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.
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Affiliation(s)
- Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Thomas Friedrich
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Vicky Oberkofler
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
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30
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Karczyński P, Orłowska A, Kępczyńska E. Two Medicago truncatula growth-promoting rhizobacteria capable of limiting in vitro growth of the Fusarium soil-borne pathogens modulate defense genes expression. PLANTA 2023; 257:118. [PMID: 37173556 PMCID: PMC10181981 DOI: 10.1007/s00425-023-04145-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
MAIN CONCLUSION PGPRs: P. fluorescens Ms9N and S. maltophilia Ll4 inhibit in vitro growth of three legume fungal pathogens from the genus Fusarium. One or both trigger up-regulation of some genes (CHIT, GLU, PAL, MYB, WRKY) in M. truncatula roots and leaves in response to soil inoculation. Pseudomonas fluorescens (referred to as Ms9N; GenBank accession No. MF618323, not showing chitinase activity) and Stenotrophomonas maltophilia (Ll4; GenBank accession No. MF624721, showing chitinase activity), previously identified as promoting growth rhizobacteria of Medicago truncatula, were found, during an in vitro experiment, to exert an inhibitory effect on three soil-borne fungi: Fusarium culmorum Cul-3, F. oxysporum 857 and F. oxysporum f. sp. medicaginis strain CBS 179.29, responsible for serious diseases of most legumes including M. truncatula. S. maltophilia was more active than P. fluorescens in suppressing the mycelium growth of two out of three Fusarium strains. Both bacteria showed β-1,3-glucanase activity which was about 5 times higher in P. fluorescens than in S. maltophilia. Upon soil treatment with a bacterial suspension, both bacteria, but particularly S. maltophilia, brought about up-regulation of plant genes encoding chitinases (MtCHITII, MtCHITIV, MtCHITV), glucanases (MtGLU) and phenylalanine ammonia lyases (MtPAL2, MtPAL4, MtPAL5). Moreover, the bacteria up-regulate some genes from the MYB (MtMYB74, MtMYB102) and WRKY (MtWRKY6, MtWRKY29, MtWRKY53, MtWRKY70) families which encode TFs in M. truncatula roots and leaves playing multiple roles in plants, including a defense response. The effect depended on the bacterium species and the plant organ. This study provides novel information about effects of two M. truncatula growth-promoting rhizobacteria strains and suggests that both have a potential to be candidates for PGPR inoculant products on account of their ability to inhibit in vitro growth of Fusarium directly and indirectly by up-regulation of some defense priming markers such as CHIT, GLU and PAL genes in plants. This is also the first study of the expression of some MYB and WRKY genes in roots and leaves of M. truncatula upon soil treatment with two PGPR suspensions.
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Affiliation(s)
- Piotr Karczyński
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
| | - Anna Orłowska
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
| | - Ewa Kępczyńska
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
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31
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Miranda de la Torre JO, Peppino Margutti MY, Lescano López I, Cambiagno DA, Alvarez ME, Cecchini NM. The Arabidopsis chromatin regulator MOM1 is a negative component of the defense priming induced by AZA, BABA and PIP. FRONTIERS IN PLANT SCIENCE 2023; 14:1133327. [PMID: 37229135 PMCID: PMC10203520 DOI: 10.3389/fpls.2023.1133327] [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: 12/28/2022] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
In plants, the establishment of broad and long-lasting immunity is based on programs that control systemic resistance and immunological memory or "priming". Despite not showing activated defenses, a primed plant induces a more efficient response to recurrent infections. Priming might involve chromatin modifications that allow a faster/stronger activation of defense genes. The Arabidopsis chromatin regulator "Morpheus Molecule 1" (MOM1) has been recently suggested as a priming factor affecting the expression of immune receptor genes. Here, we show that mom1 mutants exacerbate the root growth inhibition response triggered by the key defense priming inducers azelaic acid (AZA), β-aminobutyric acid (BABA) and pipecolic acid (PIP). Conversely, mom1 mutants complemented with a minimal version of MOM1 (miniMOM1 plants) are insensitive. Moreover, miniMOM1 is unable to induce systemic resistance against Pseudomonas sp. in response to these inducers. Importantly, AZA, BABA and PIP treatments reduce the MOM1 expression, but not miniMOM1 transcript levels, in systemic tissues. Consistently, several MOM1-regulated immune receptor genes are upregulated during the activation of systemic resistance in WT plants, while this effect is not observed in miniMOM1. Taken together, our results position MOM1 as a chromatin factor that negatively regulates the defense priming induced by AZA, BABA and PIP.
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Affiliation(s)
- Julián O. Miranda de la Torre
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Micaela Y. Peppino Margutti
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ignacio Lescano López
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Damián Alejandro Cambiagno
- Unidad de Estudios Agropecuarios (UDEA), Instituto Nacional de Tecnología Agropecuaria (INTA)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María E. Alvarez
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Nicolás M. Cecchini
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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32
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Hönig M, Roeber VM, Schmülling T, Cortleven A. Chemical priming of plant defense responses to pathogen attacks. FRONTIERS IN PLANT SCIENCE 2023; 14:1146577. [PMID: 37223806 PMCID: PMC10200928 DOI: 10.3389/fpls.2023.1146577] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Plants can acquire an improved resistance against pathogen attacks by exogenous application of natural or artificial compounds. In a process called chemical priming, application of these compounds causes earlier, faster and/or stronger responses to pathogen attacks. The primed defense may persist over a stress-free time (lag phase) and may be expressed also in plant organs that have not been directly treated with the compound. This review summarizes the current knowledge on the signaling pathways involved in chemical priming of plant defense responses to pathogen attacks. Chemical priming in induced systemic resistance (ISR) and systemic acquired resistance (SAR) is highlighted. The roles of the transcriptional coactivator NONEXPRESSOR OF PR1 (NPR1), a key regulator of plant immunity, induced resistance (IR) and salicylic acid signaling during chemical priming are underlined. Finally, we consider the potential usage of chemical priming to enhance plant resistance to pathogens in agriculture.
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Affiliation(s)
- Martin Hönig
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany
- Department of Chemical Biology, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Venja M. Roeber
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany
| | - Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany
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33
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García-Murillo L, Valencia-Lozano E, Priego-Ranero NA, Cabrera-Ponce JL, Duarte-Aké FP, Vizuet-de-Rueda JC, Rivera-Toro DM, Herrera-Ubaldo H, de Folter S, Alvarez-Venegas R. CRISPRa-mediated transcriptional activation of the SlPR-1 gene in edited tomato plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111617. [PMID: 36731748 DOI: 10.1016/j.plantsci.2023.111617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/11/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
With the continuous deterioration of arable land due to an ever-growing population, improvement of crops and crop protection have a fundamental role in maintaining and increasing crop productivity. Alternatives to the use of pesticides encompass the use of biological control agents, generation of new resistant crop cultivars, the application of plant activator agrochemicals to enhance plant defenses, and the use of gene editing techniques, like the CRISPR-Cas system. Here, we test the hypothesis that epigenome editing, via CRISPR activation (CRISPRa), activate tomato plant defense genes to confer resistance against pathogen attack. We provide evidence that edited tomato plants for the PATHOGENESIS-RELATED GENE 1 gene (SlPR-1) show enhanced disease resistance to Clavibacter michiganensis subsp. michiganensis infection. Resistance was assessed by evaluating disease progression and symptom appearance, pathogen accumulation, and changes in SlPR-1 gene expression at different time points. We determined that CRISPRa-edited plants develop enhanced disease-resistant to the pathogen without altering their agronomic characteristics and, above all, preventing the advancement of disease symptoms, stem canker, and plant death.
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Affiliation(s)
- Leonardo García-Murillo
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Eliana Valencia-Lozano
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Nicolás Alberto Priego-Ranero
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - José Luis Cabrera-Ponce
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Fátima Patricia Duarte-Aké
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Juan Carlos Vizuet-de-Rueda
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Diana Marcela Rivera-Toro
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Humberto Herrera-Ubaldo
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - Raúl Alvarez-Venegas
- Center for Research and Advanced Studies of the National Polytechnic Institute, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico.
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34
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Holness S, Bechtold U, Mullineaux P, Serino G, Vittorioso P. Highlight Induced Transcriptional Priming against a Subsequent Drought Stress in Arabidopsis thaliana. Int J Mol Sci 2023; 24:6608. [PMID: 37047580 PMCID: PMC10095447 DOI: 10.3390/ijms24076608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
In plants, priming allows a more rapid and robust response to recurring stresses. However, while the nature of plant response to a single stress can affect the subsequent response to the same stress has been deeply studied, considerably less is known on how the priming effect due to one stress can help plants cope with subsequent different stresses, a situation that can be found in natural ecosystems. Here, we investigate the potential priming effects in Arabidopsis plants subjected to a high light (HL) stress followed by a drought (D) stress. The cross-stress tolerance was assessed at the physiological and molecular levels. Our data demonstrated that HL mediated transcriptional priming on the expression of specific stress response genes. Furthermore, this priming effect involves both ABA-dependent and ABA-independent responses, as also supported by reduced expression of these genes in the aba1-3 mutant compared to the wild type. We have also assessed several physiological parameters with the aim of seeing if gene expression coincides with any physiological changes. Overall, the results from the physiological measurements suggested that these physiological processes did not experience metabolic changes in response to the stresses. In addition, we show that the H3K4me3 epigenetic mark could be a good candidate as an epigenetic mark in priming response. Overall, our results help to elucidate how HL-mediated priming can limit D-stress and enhance plant responses to stress.
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Affiliation(s)
- Soyanni Holness
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Ulrike Bechtold
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | | | - Giovanna Serino
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Paola Vittorioso
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy
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Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
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Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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36
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Kloc M, Kubiak JZ, Zdanowski R, Ghobrial RM. Memory Macrophages. Int J Mol Sci 2022; 24:ijms24010038. [PMID: 36613481 PMCID: PMC9819859 DOI: 10.3390/ijms24010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Immunological memory is a crucial part of the immune defense that allows organisms to respond against previously encountered pathogens or other harmful factors. Immunological memory is based on the establishment of epigenetic modifications of the genome. The ability to memorize encounters with pathogens and other harmful factors and mount enhanced defense upon subsequent encounters is an evolutionarily ancient mechanism operating in all animals and plants. However, the term immunological memory is usually restricted to the organisms (invertebrates and vertebrates) possessing the immune system. The mammalian immune system, with innate and adaptive branches, is the most sophisticated among vertebrates. The concept of innate memory and memory macrophages is relatively new and thus understudied. We introduce the concept of immunological memory and describe types of memory in different species and their evolutionary status. We discuss why the traditional view of innate immune cells as the first-line defenders is too restrictive and how the innate immune cells can accumulate and retain immunologic memory. We describe how the initial priming leads to chromatin remodeling and epigenetic changes, which allow memory macrophage formation. We also summarize what is currently known about the mechanisms underlying development of memory macrophages; their molecular and metabolic signature and surface markers; and how they may contribute to immune defense, diseases, and organ transplantation.
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Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
- Correspondence:
| | - Jacek Z. Kubiak
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Robert Zdanowski
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Rafik M. Ghobrial
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
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Ramakrishnan M, Zhang Z, Mullasseri S, Kalendar R, Ahmad Z, Sharma A, Liu G, Zhou M, Wei Q. Epigenetic stress memory: A new approach to study cold and heat stress responses in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1075279. [PMID: 36570899 PMCID: PMC9772030 DOI: 10.3389/fpls.2022.1075279] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 05/28/2023]
Abstract
Understanding plant stress memory under extreme temperatures such as cold and heat could contribute to plant development. Plants employ different types of stress memories, such as somatic, intergenerational and transgenerational, regulated by epigenetic changes such as DNA and histone modifications and microRNAs (miRNA), playing a key role in gene regulation from early development to maturity. In most cases, cold and heat stresses result in short-term epigenetic modifications that can return to baseline modification levels after stress cessation. Nevertheless, some of the modifications may be stable and passed on as stress memory, potentially allowing them to be inherited across generations, whereas some of the modifications are reactivated during sexual reproduction or embryogenesis. Several stress-related genes are involved in stress memory inheritance by turning on and off transcription profiles and epigenetic changes. Vernalization is the best example of somatic stress memory. Changes in the chromatin structure of the Flowering Locus C (FLC) gene, a MADS-box transcription factor (TF), maintain cold stress memory during mitosis. FLC expression suppresses flowering at high levels during winter; and during vernalization, B3 TFs, cold memory cis-acting element and polycomb repressive complex 1 and 2 (PRC1 and 2) silence FLC activation. In contrast, the repression of SQUAMOSA promoter-binding protein-like (SPL) TF and the activation of Heat Shock TF (HSFA2) are required for heat stress memory. However, it is still unclear how stress memory is inherited by offspring, and the integrated view of the regulatory mechanisms of stress memory and mitotic and meiotic heritable changes in plants is still scarce. Thus, in this review, we focus on the epigenetic regulation of stress memory and discuss the application of new technologies in developing epigenetic modifications to improve stress memory.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhijun Zhang
- Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guohua Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
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Patil V, Nandi AK. POWERDRESS positively regulates systemic acquired resistance in Arabidopsis. PLANT CELL REPORTS 2022; 41:2351-2362. [PMID: 36152035 DOI: 10.1007/s00299-022-02926-2] [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: 06/09/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
PWR, an epigenetic regulator, and PIF4, a transcription factor coordinately regulate both local resistance and systemic acquired resistance in Arabidopsis. A plant that gets infected once becomes resistant to subsequent infections through the development of systemic acquired resistance (SAR). Primary-infected tissues generate mobile signals that travel to systemic tissues and cause epigenetic changes associated with the SAR activation. Epigenetic regulators and the process of infection memory development are largely obscure for plants. POWERDRESS (PWR), a SANT domain-containing histone deacetylation (HDAC) promoting gene, is essential for thermomorphogenesis. Here we show that PWR is required for the SAR activation in Arabidopsis. The pwr mutants in Ler and Col-0 background possess normal local resistance but are defective in SAR. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) genetically interacts with PWR for flowering and thermomorphogenesis and is a negative regulator of basal immunity. We found a cooperative function for suppressing basal immunity and SAR activation by PIF4 and PWR, respectively. PWR promotes the expression of SA biosynthesis genes and the accumulation of SA in the systemic tissues. RSI1/FLD, which influences histone methylation and acetylation, is essential to infection memory development in Arabidopsis. Our results show that PWR and RSI1 positively regulate each other's expression. Exogenous application of HDAC inhibitor sodium butyrate abolishes SAR-mediated SA accumulation, expression of PR1 gene, and protection against pathogens after challenge inoculation. The results indicate the possibility of the involvement of HDAC activity of PWR in the formation of infection memory development in Arabidopsis.
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Affiliation(s)
- Vishal Patil
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India
| | - Ashis Kumar Nandi
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India.
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Herath V, Verchot J. Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato ( Solanum tuberosum L.). Int J Mol Sci 2022; 23:ijms232213795. [PMID: 36430273 PMCID: PMC9696714 DOI: 10.3390/ijms232213795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
We treated potato (Solanum tuberosum L.) plantlets with TM and performed gene expression studies to identify genome-wide changes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). An extensive network of responses was identified, including chromatin remodeling, transcriptional reprogramming, as well as changes in the structural components of the endomembrane network system. Limited genome-wide changes in alternative RNA splicing patterns of protein-coding transcripts were also discovered. Significant changes in RNA metabolism, components of the translation machinery, as well as factors involved in protein folding and maturation occurred, which included a broader set of genes than expected based on Arabidopsis research. Antioxidant defenses and oxygen metabolic enzymes are differentially regulated, which is expected of cells that may be experiencing oxidative stress or adapting to protect proteins from oxidation. Surges in protein kinase expression indicated early signal transduction events. This study shows early genomic responses including an array of differentially expressed genes that have not been reported in Arabidopsis. These data describe novel ER stress responses in a solanaceous host.
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Affiliation(s)
- Venura Herath
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA
- Correspondence: ; Tel.: +1-979-568-6369
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40
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Zhou H, Hua J, Zhang J, Luo S. Negative Interactions Balance Growth and Defense in Plants Confronted with Herbivores or Pathogens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12723-12732. [PMID: 36165611 DOI: 10.1021/acs.jafc.2c04218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plants have evolved a series of defensive mechanisms against pathogens and herbivores, but the defense response always leads to decreases in growth or reproduction, which has serious implications for agricultural production. Growth and defense are negatively regulated not only through metabolic consumption but also through the antagonism of different phytohormones, such as jasmonic acid (JA) and salicylic acid (SA). Meanwhile, plants can limit the expression of defensive metabolites to reduce the costs of defense by producing constitutive defenses such as glandular trichomes or latex and accumulating specific metabolites, determining the activation of plant defense or the maintenance of plant growth. Interestingly, plant defense pathways might be prepared in advance which may be transmitted to descendants. Plants can also use external organisms to protect themselves, thus minimizing the costs of defense. In addition, plant relatives exhibit cooperation to deal with pathogens and herbivores, which is also a way to regulate growth and defense.
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Affiliation(s)
- Huiwen Zhou
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Juan Hua
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Jiaming Zhang
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Shihong Luo
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
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Bvindi C, Tang L, Lee S, Patrick RM, Yee ZR, Mengiste T, Li Y. Histone methyltransferases SDG33 and SDG34 regulate organ-specific nitrogen responses in tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:1005077. [PMID: 36311072 PMCID: PMC9606235 DOI: 10.3389/fpls.2022.1005077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Histone posttranslational modifications shape the chromatin landscape of the plant genome and affect gene expression in response to developmental and environmental cues. To date, the role of histone modifications in regulating plant responses to environmental nutrient availability, especially in agriculturally important species, remains largely unknown. We describe the functions of two histone lysine methyltransferases, SET Domain Group 33 (SDG33) and SDG34, in mediating nitrogen (N) responses of shoots and roots in tomato. By comparing the transcriptomes of CRISPR edited tomato lines sdg33 and sdg34 with wild-type plants under N-supplied and N-starved conditions, we uncovered that SDG33 and SDG34 regulate overlapping yet distinct downstream gene targets. In response to N level changes, both SDG33 and SDG34 mediate gene regulation in an organ-specific manner: in roots, SDG33 and SDG34 regulate a gene network including Nitrate Transporter 1.1 (NRT1.1) and Small Auxin Up-regulated RNA (SAUR) genes. In agreement with this, mutations in sdg33 or sdg34 abolish the root growth response triggered by an N-supply; In shoots, SDG33 and SDG34 affect the expression of photosynthesis genes and photosynthetic parameters in response to N. Our analysis thus revealed that SDG33 and SDG34 regulate N-responsive gene expression and physiological changes in an organ-specific manner, thus presenting previously unknown candidate genes as targets for selection and engineering to improve N uptake and usage in crop plants.
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Affiliation(s)
- Carol Bvindi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Liang Tang
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ryan M. Patrick
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Zheng Rong Yee
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ying Li
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
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42
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Kang H, Fan T, Wu J, Zhu Y, Shen WH. Histone modification and chromatin remodeling in plant response to pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:986940. [PMID: 36262654 PMCID: PMC9574397 DOI: 10.3389/fpls.2022.986940] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
As sessile organisms, plants are constantly exposed to changing environments frequently under diverse stresses. Invasion by pathogens, including virus, bacterial and fungal infections, can severely impede plant growth and development, causing important yield loss and thus challenging food/feed security worldwide. During evolution, plants have adapted complex systems, including coordinated global gene expression networks, to defend against pathogen attacks. In recent years, growing evidences indicate that pathogen infections can trigger local and global epigenetic changes that reprogram the transcription of plant defense genes, which in turn helps plants to fight against pathogens. Here, we summarize up plant defense pathways and epigenetic mechanisms and we review in depth current knowledge's about histone modifications and chromatin-remodeling factors found in the epigenetic regulation of plant response to biotic stresses. It is anticipated that epigenetic mechanisms may be explorable in the design of tools to generate stress-resistant plant varieties.
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Affiliation(s)
- Huijia Kang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Tianyi Fan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
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Song N, Lin J, Liu X, Liu Z, Liu D, Chu W, Li J, Chen Y, Chang S, Yang Q, Liu X, Guo W, Xin M, Yao Y, Peng H, Ni Z, Xie C, Sun Q, Hu Z. Histone acetyltransferase TaHAG1 interacts with TaPLATZ5 to activate TaPAD4 expression and positively contributes to powdery mildew resistance in wheat. THE NEW PHYTOLOGIST 2022; 236:590-607. [PMID: 35832009 PMCID: PMC9795918 DOI: 10.1111/nph.18372] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/06/2022] [Indexed: 05/24/2023]
Abstract
Plants have evolved a two-branched innate immune system to detect and cope with pathogen attack, which are initiated by cell-surface and intracellular immune receptors leading to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), respectively. A core transducer including PAD4-EDS1 node is proposed as the convergence point for a two-tiered immune system in conferring pathogen immunity. However, the transcriptional regulatory mechanisms controlling expression of these key transducers remain largely unknown. Here, we identified histone acetyltransferase TaHAG1 as a positive regulator of powdery mildew resistance in wheat. TaHAG1 regulates expression of key transducer gene TaPAD4 and promotes SA and reactive oxygen species accumulation to accomplish resistance to Bgt infection. Moreover, overexpression and CRISPR-mediated knockout of TaPAD4 validate its role in wheat powdery mildew resistance. Furthermore, TaHAG1 physically interacts with TaPLATZ5, a plant-specific zinc-binding protein. TaPLATZ5 directly binds to promoter of TaPAD4 and together with TaHAG1 to potentiate the expression of TaPAD4 by increasing the levels of H3 acetylation. Our study revealed a key transcription regulatory node in which TaHAG1 acts as an epigenetic modulator and interacts with TaPLATZ5 that confers powdery mildew resistance in wheat through activating a convergence point gene between PTI and ETI, which could be effective for genetic improvement of disease resistance in wheat and other crops.
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Affiliation(s)
- Na Song
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Jingchen Lin
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Xingbei Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zehui Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Debiao Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Wei Chu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Jinpeng Li
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Shumin Chang
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Qun Yang
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Xiaoyu Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
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Shen Y, Chi Y, Lu S, Lu H, Shi L. Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1009723. [PMID: 36226276 PMCID: PMC9549339 DOI: 10.3389/fpls.2022.1009723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Post-translational histone modifications play important roles in regulating chromatin structure and transcriptional regulation. Histone 3 lysine 4 trimethylation (H3K4me3) is a prominent histone modification mainly associated with gene activation. Here we showed that a histone demethylase, JMJ15, belonging to KDM5/JARID group, is involved in salt stress response in Arabidopsis thaliana. Jmj15 loss-of-function mutants displayed increased sensitivity to salt stress. Moreover, knockout of JMJ15 impaired the salt responsive gene expression program and affected H3K4me3 levels of many stress-related genes under salt-stressed condition. Importantly, we demonstrated that JMJ15 regulated the expression level of two WRKY transcription factors, WRKY46 and WRKY70, which were negatively involved in abiotic stress tolerance. Furthermore, JMJ15 directly bound to and demethylated H3K4me3 mark in the promoter and coding regions of WRKY46 and WRKY70, thereby repressing these two WRKY gene expression under salt stress. Overall, our study revealed a novel molecular function of the histone demethylase JMJ15 under salt stress in plants.
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Affiliation(s)
- Yuan Shen
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Yuhao Chi
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Shun Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Huijuan Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Lei Shi
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
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Banday ZZ, Cecchini NM, Speed DJ, Scott AT, Parent C, Hu CT, Filzen RC, Agbo E, Greenberg JT. Friend or foe: Hybrid proline-rich proteins determine how plants respond to beneficial and pathogenic microbes. PLANT PHYSIOLOGY 2022; 190:860-881. [PMID: 35642916 PMCID: PMC9434206 DOI: 10.1093/plphys/kiac263] [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: 04/12/2022] [Accepted: 05/08/2022] [Indexed: 05/21/2023]
Abstract
Plant plastids generate signals, including some derived from lipids, that need to be mobilized to effect signaling. We used informatics to discover potential plastid membrane proteins involved in microbial responses in Arabidopsis (Arabidopsis thaliana). Among these are proteins co-regulated with the systemic immunity component AZELAIC ACID INDUCED 1, a hybrid proline-rich protein (HyPRP), and HyPRP superfamily members. HyPRPs have a transmembrane domain, a proline-rich region (PRR), and a lipid transfer protein domain. The precise subcellular location(s) and function(s) are unknown for most HyPRP family members. As predicted by informatics, a subset of HyPRPs has a pool of proteins that target plastid outer envelope membranes via a mechanism that requires the PRR. Additionally, two HyPRPs may be associated with thylakoid membranes. Most of the plastid- and nonplastid-localized family members also have pools that localize to the endoplasmic reticulum, plasma membrane, or plasmodesmata. HyPRPs with plastid pools regulate, positively or negatively, systemic immunity against the pathogen Pseudomonas syringae. HyPRPs also regulate the interaction with the plant growth-promoting rhizobacteria Pseudomonas simiae WCS417 in the roots to influence colonization, root system architecture, and/or biomass. Thus, HyPRPs have broad and distinct roles in immunity, development, and growth responses to microbes and reside at sites that may facilitate signal molecule transport.
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Affiliation(s)
- Zeeshan Z Banday
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | | | - DeQuantarius J Speed
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Allison T Scott
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | | | - Ciara T Hu
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rachael C Filzen
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Elinam Agbo
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
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Systemic acquired resistance-associated transport and metabolic regulation of salicylic acid and glycerol-3-phosphate. Essays Biochem 2022; 66:673-681. [PMID: 35920211 DOI: 10.1042/ebc20210098] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022]
Abstract
Systemic acquired resistance (SAR), a type of long-distance immunity in plants, provides long-lasting resistance to a broad spectrum of pathogens. SAR is thought to involve the rapid generation and systemic transport of a mobile signal that prepares systemic parts of the plant to better resist future infections. Exploration of the molecular mechanisms underlying SAR have identified multiple mobile regulators of SAR in the last few decades. Examination of the relationship among several of these seemingly unrelated molecules depicts a forked pathway comprising at least two branches of equal importance to SAR. One branch is regulated by the plant hormone salicylic acid (SA), and the other culminates (based on current knowledge) with the phosphorylated sugar derivative, glycerol-3-phosphate (G3P). This review summarizes the activities that contribute to pathogen-responsive generation of SA and G3P and the components that regulate their systemic transport during SAR.
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Immune priming in plants: from the onset to transgenerational maintenance. Essays Biochem 2022; 66:635-646. [PMID: 35822618 PMCID: PMC9528079 DOI: 10.1042/ebc20210082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 12/24/2022]
Abstract
Enhancing plant resistance against pests and diseases by priming plant immunity is an attractive concept for crop protection because it provides long-lasting broad-spectrum protection against pests and diseases. This review provides a selected overview of the latest advances in research on the molecular, biochemical and epigenetic drivers of plant immune priming. We review recent findings about the perception and signalling mechanisms controlling the onset of priming by the plant stress metabolite β-aminobutyric acid. In addition, we review the evidence for epigenetic regulation of long-term maintenance of priming and discuss how stress-induced reductions in DNA hypomethylation at transposable elements can prime defence genes. Finally, we examine how priming can be exploited in crop protection and articulate the opportunities and challenges of translating research results from the Arabidopsis model system to crops.
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Griebel T, Schütte D, Ebert A, Nguyen HH, Baier M. Cold Exposure Memory Reduces Pathogen Susceptibility in Arabidopsis Based on a Functional Plastid Peroxidase System. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:627-637. [PMID: 35345887 DOI: 10.1094/mpmi-11-21-0283-fi] [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] [Indexed: 06/14/2023]
Abstract
Chloroplasts serve as cold priming hubs modulating the transcriptional response of Arabidopsis thaliana to a second cold stimulus for several days by postcold accumulation of thylakoid ascorbate peroxidases (tAPX). In an attempt to investigate cross-priming effects of cold on plant pathogen protection, we show here that such a single 24-h cold treatment at 4°C decreased the susceptibility of Arabidopsis to virulent Pseudomonas syringae pv. tomato DC3000 but did not alter resistance against the avirulent P. syringae pv. tomato avRPM1 and P. syringae pv. tomato avrRPS4 strains or the effector-deficient P. syringae pv. tomato strain hrcC-. The effect of cold priming against P. syringae pv. tomato was active immediately after cold exposure and memorized for at least 5 days. The priming benefit was established independent of the immune regulator Enhanced Disease Susceptibility 1 (EDS1) or activation of the immune-related genes NHL10, FRK1, ICS1 and PR1 but required thylakoid-bound as well as stromal ascorbate peroxidase activities because the effect was absent or weak in corresponding knock-out-lines. Suppression of tAPX postcold regulation in a conditional-inducible tAPX-RNAi line led to increased bacterial growth numbers. This highlights that the plant immune system benefits from postcold regeneration of the protective chloroplast peroxidase system.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Thomas Griebel
- Plant Physiology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Dominic Schütte
- Plant Physiology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Alina Ebert
- Plant Physiology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - H Hung Nguyen
- Plant Physiology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
| | - Margarete Baier
- Plant Physiology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany
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Liu H, Able AJ, Able JA. Priming crops for the future: rewiring stress memory. TRENDS IN PLANT SCIENCE 2022; 27:699-716. [PMID: 34906381 DOI: 10.1016/j.tplants.2021.11.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 05/12/2023]
Abstract
The agricultural sector must produce resilient and climate-smart crops to meet the increasing needs of global food production. Recent advancements in elucidating the mechanistic basis of plant stress memory have provided new opportunities for crop improvement. Stress memory-coordinated changes at the organismal, cellular, and various omics levels prepare plants to be more responsive to reoccurring stress within or across generation(s). The exposure to a primary stress, or stress priming, can also elicit a beneficial impact when encountering a secondary abiotic or biotic stress through the convergence of synergistic signalling pathways, referred to as cross-stress tolerance. 'Rewired plants' with stress memory provide a new means to stimulate adaptable stress responses, safeguard crop reproduction, and engineer climate-smart crops for the future.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
| | - Amanda J Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
| | - Jason A Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia.
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Roles of RNA silencing in viral and non-viral plant immunity and in the crosstalk between disease resistance systems. Nat Rev Mol Cell Biol 2022; 23:645-662. [PMID: 35710830 DOI: 10.1038/s41580-022-00496-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
RNA silencing is a well-established antiviral immunity system in plants, in which small RNAs guide Argonaute proteins to targets in viral RNA or DNA, resulting in virus repression. Virus-encoded suppressors of silencing counteract this defence system. In this Review, we discuss recent findings about antiviral RNA silencing, including the movement of RNA through plasmodesmata and the differentiation between plant self and viral RNAs. We also discuss the emerging role of RNA silencing in plant immunity against non-viral pathogens. This immunity is mediated by transkingdom movement of RNA into and out of the infected plant cells in vesicles or as extracellular nucleoproteins and, like antiviral immunity, is influenced by the silencing suppressors encoded in the pathogens' genomes. Another effect of RNA silencing on general immunity involves host-encoded small RNAs, including microRNAs, that regulate NOD-like receptors and defence signalling pathways in the innate immunity system of plants. These RNA silencing pathways form a network of processes with both positive and negative effects on the immune systems of plants.
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