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Authors: Ping Yun, Cengiz Kaya and Sergey Shabala.
The Crop Journal (2024)
Abstract: "Salinity stress is a major environmental stress affecting crop productivity, and its negative impact on global food security is only going to increase, due to current climate trends. Salinity tolerance was present in wild crop relatives but significantly weakened during domestication. Regaining it back requires a good understanding of molecular mechanisms and traits involved in control of plant ionic and ROS homeostasis. This review summarizes our current knowledge on the role of major plant hormones (auxin, cytokinins, abscisic acid, salicylic acid, and jasmonate) in plants adaptation to soil salinity. We firstly discuss the role of hormones in controlling root tropisms, root growth and architecture (primary root elongation, meristematic activity, lateral root development, and root hairs formation). Hormone-mediated control of uptake and sequestration of key inorganic ions (sodium, potassium, and calcium) is then discussed followed by regulation of cell redox balance and ROS signaling in salt-stressed roots. Finally, the role of epigenetic alterations such as DNA methylation and histone modifications in control of plant ion and ROS homeostasis and signaling is discussed. This data may help develop novel strategies for breeding and cultivating salt-tolerant crops and improving agricultural productivity in saline regions."
Authors: Xiaoxiao Li, Chuyu Lin, Chenghao Lan and Zeng Tao.
Journal of Experimental Botany (2024)
Abstract: "The timing of the developmental transition from the vegetative to the reproductive stages is critical for angiosperm and fine-tuned by the integration of endogenous factors and external environmental cues to ensure proper and successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, which may be mediated by plant hormones which coordinate their flowering time. Endogenous and exogenous phytohormones such as gibberellin (GA), auxin, cytokinin (CK), jasmonate (JA), abscisic acid (ABA), ethylene (ET), brassinosteroids (BR) and the cross-talk among them are critical for the precise regulating of flowering time. Recent studies on the model flowering plant Arabidopsis thaliana revealed that diverse transcription factors and epigenetic regulators play key roles in the phytohormones that regulate floral transition. This review aims to summarize current knowledge on the genetic and epigenetic mechanisms that underlying the phytohormone control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology."
Authors: Pascal Hunziker and Thomas Greb.
Annual Review of Plant Biology (2024)
Abstract: "Plant vascular tissues are crucial for the long-distance transport of water, nutrients, and a multitude of signal molecules throughout the plant body and, therefore, central to plant growth and development. The intricate development of vascular tissues is orchestrated by unique populations of dedicated stem cells integrating endogenous as well as environmental cues. This review summarizes our current understanding of vascular-related stem cell biology and of vascular tissue differentiation. We present an overview of the molecular and cellular mechanisms governing the maintenance and fate determination of vascular stem cells and highlight the interplay between intrinsic and external cues. In this context, we emphasize the role of transcription factors, hormonal signaling, and epigenetic modifications. We also discuss emerging technologies and the large repertoire of cell types associated with vascular tissues, which have the potential to provide unprecedented insights into cellular specialization and anatomical adaptations to distinct ecological niches."
Authors: Tao Zhu, Chuangqi Wei, Yaoguang Yu, Zhenzhen Zhang, Jiameng Zhu, Zhenwei Liang, Xin Song, Wei Fu, Yuhai Cui, Zhi-Yong Wang and Chenlong Li.
Developmental Cell (2024)
Editor's view: The mechanism that dictates the transcriptional activation ability of the brassinosteroid (BR) hormone remains largely unclear. Zhu et al. find that the BAS-chromatin-remodeling subcomplexes are major determinants of the transcriptional activation activity of the BR signaling pathway for allowing plants to shape their growth and development trajectory.
Highlights • Brassinosteroid has dual roles in reshaping the chromatin accessibility landscape • BZR1 physically interacts with the BAS complex • The BAS complex determines BR-induced transcriptional activation • BZR1 recruits the BAS complex for chromatin opening and BR-mediated skotomorphogenesis
Abstract: "Brassinosteroid (BR) signaling leads to the nuclear accumulation of the BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor, which plays dual roles in activating or repressing the expression of thousands of genes. BZR1 represses gene expression by recruiting histone deacetylases, but how it activates transcription of BR-induced genes remains unclear. Here, we show that BR reshapes the genome-wide chromatin accessibility landscape, increasing the accessibility of BR-induced genes and reducing the accessibility of BR-repressed genes in Arabidopsis. BZR1 physically interacts with the BRAHMA-associated SWI/SNF (BAS)-chromatin-remodeling complex on the genome and selectively recruits the BAS complex to BR-activated genes. Depletion of BAS abrogates the capacities of BZR1 to increase chromatin accessibility, activate gene expression, and promote cell elongation without affecting BZR1’s ability to reduce chromatin accessibility and expression of BR-repressed genes. Together, these data identify that BZR1 recruits the BAS complex to open chromatin and to mediate BR-induced transcriptional activation of growth-promoting genes.
Authors: Jordan Powers, Xing Zhang, Andres V. Reyes, Raul Zavaliev, Shou-Ling Xu and Xinnian Dong.
bioRxiv (2024)
Abstract: "For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for both basal and systemic acquired resistance (SAR). SA activates these immune responses by reprogramming up to 20% of the transcriptome through the function of NPR1. However, components in the NPR1-signaling hub, which appears as nuclear condensates, and the NPR1-signaling cascade remained elusive due to difficulties in studying transcriptional cofactors whose chromatin associations are often indirect and transient. To overcome this challenge, we applied TurboID to divulge the NPR1-proxiome, which detected almost all known NPR1-interactors as well as new components of transcription-related complexes. Testing of new components showed that chromatin remodeling and histone demethylation contribute to SA-induced resistance. Globally, NPR1-proxiome shares a striking similarity to GBPL3-proxiome involved in SA synthesis, except associated transcription factors (TFs), suggesting that common regulatory modules are recruited to reprogram specific transcriptomes by transcriptional cofactors, like NPR1, through binding to unique TFs. Stepwise greenCUT&RUN analyses showed that, upon SA-induction, NPR1 initiates the transcriptional cascade primarily through association with TGA TFs to induce expression of secondary TFs, predominantly WRKYs. WRKY54 and WRKY70 then play a major role in inducing immune-output genes without interacting with NPR1 at the chromatin. Moreover, a loss of NPR1 condensate formation decreases its chromatin-association and transcriptional activity, indicating the importance of condensates in organizing the NPR1-signaling hub and initiating the transcriptional cascade. This study demonstrates how combinatorial applications of TurboID, and stepwise greenCUT&RUN transcend traditional genetic methods to globally map signaling hubs and transcriptional cascades."
Author: Carlisle Bascom, Jr.
The Plant Cell (2024)
Excerpts: "Myriad genes control plant size and development in Arabidopsis (A. thaliana), including those encoding the BASIC PENTACYSTEINE (BPC) class of transcription factors (Monfared et al. 2011). However, whether BPCs regulate development in woody plants is an open question. In this issue, Haiyan Zhao and colleagues (Zhao et al. 2024) reveal some details of the genetic regulation of dwarfism in apple trees, Malus domestica. Through genetics, bioinformatics, and biochemical assays, Zhao and colleagues elucidated a key molecular mechanism for plant dwarfism (see Figure)."
"Histone trimethylation (H3K27me3) results in repression of target genes (Cai et al. 2021). Here, the authors found that H3K27me3 enrichment was significantly increased at MdYUC2a and 6b loci in OX plants. H3K27me3 modifications are facilitated by a large complex of proteins known as the polycomb group. The author used biochemical techniques to demonstrate that MdBPC2 interacts with the polycomb group member LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Indeed, MdYUC2a and 6b loci are enriched with MdLHP1 (see Figure). With this result, the authors proposed a straight-forward model whereby MdBPC2 protein recruits LHP1 protein to the promoters of a subset of YUCCA genes to repress their expression, thereby reducing the amount of auxin produced. In dwarf rootstocks, increased MdBPC2 expression results in much less MdYUC2a and 6b enzymes, and shorter, auxin-deficient plants (see Figure). Moving forward, one can see BPCs as an attractive target for crop breeding programs where dwarf plants are the goal."
Authors: Mei Du, Yongchao Zhu, Hong Nan, Yujia Zhou and Xuejun Pan.
Scientia Horticulturae (2024)
Highlights: • The sugar content, species, and proportion play a key role in determining fruit flavor. • Transcription factors (TFs) play a crucial role in regulating sugar content and metabolism in fruits. • Epigenetic modifications, such as DNA methylation and histone modifications, also contribute to the regulation of sugar metabolism in fruits. • Phytohormones, including abscisic acid, gibberellin, and auxin, have a significant impact on sugar metabolism in fruits. • Environmental factors, such as light, temperature, water, and mineral elements, can influence the sugar metabolism of fruits.
Abstract: "The sugar content, species, and proportion play a vital role in determining the fruit flavor, and their regulation is influenced by various factors, including transcription factors (TFs), epigenetic modifications, phytohormones, and environmental conditions. Numerous TFs have been identified as key regulators of sugar metabolism through their control over the expression of genes involved in sugar biosynthesis and transport. Epigenetic modifications, such as DNA methylation, histone modifications, and non-coding RNAs, also play a significant role in regulating sugar metabolism by maintaining genome architecture and modulating gene expression. Moreover, the metabolic process of sugar is significantly influenced by phytohormones, including abscisic acid, gibberellin, auxin, ethylene, salicylic acid, jasmonate, brassinosteroid, strigolactone, and melatonin. Additionally, environmental factors such as light, temperature, water, and mineral elements can exert an impact on sugar metabolism. This review offers a comprehensive examination of the regulatory mechanisms governing sugar metabolism, encompassing transcriptional, epigenetic, and phytohormonal perspectives, as well as other factors that affect various aspects of fruit metabolism. The innovative aspect of this review lies in its comprehensive and integrated analysis of the multiple factors that contribute to the regulation of sugar metabolism in fruits. Understanding these regulatory mechanisms is of great significance for improving fruit quality and flavor."
Authors: Yequn Wu, Jiaqi Hou, Ruifei Ren, Zhenfei Chen, Mengxia Yue, Le Li, Haoli Hou, Xueke Zheng and Lijia Li.
BMC Plant Biology (2023)
Abstract: "Background - The aleurone layer is a part of many plant seeds, and during seed germination, aleurone cells undergo PCD, which is promoted by GA from the embryo. However, the numerous components of the GA signaling pathway that mediate PCD of the aleurone layers remain to be identified. Few genes and transcriptomes have been studied thus far in aleurone layers to improve our understanding of how PCD occurs and how the regulatory mechanism functions during PCD. Our previous studies have shown that histone deacetylases (HDACs) are required in GA-induced PCD of aleurone layer. To further explore the molecular mechanisms by which epigenetic modifications regulate aleurone PCD, we performed a global comparative transcriptome analysis of embryoless aleurones treated with GA or histone acetylase (HAT) inhibitors. Results - In this study, a total of 7,919 differentially expressed genes (DEGs) were analyzed, 2,554 DEGs of which were found to be common under two treatments. These identified DEGs were involved in various biological processes, including DNA methylation, lipid metabolism and ROS signaling. Further investigations revealed that inhibition of DNA methyltransferases prevented aleurone PCD, suggesting that active DNA methylation plays a role in regulating aleurone PCD. GA or HAT inhibitor induced lipoxygenase gene expression, leading to lipid degradation, but this process was not affected by DNA methylation. However, DNA methylation inhibitor could regulate ROS-related gene expression and inhibit GA-induced production of hydrogen peroxide (H2O2). Conclusion - Overall, linking of lipoxygenase, DNA methylation, and H2O2 may indicate that GA-induced higher HDAC activity in aleurones causes breakdown of lipids via regulating lipoxygenase gene expression, and increased DNA methylation positively mediates H2O2 production; thus, DNA methylation and lipid metabolism pathways may represent an important and complex signaling network in maize aleurone PCD."
Authors: Junjie Li, Qi Li, Wentao Wang, Xinran Zhang, Chen Chu, Xintian Tang, Bo Zhu, Lizhong Xiong, Yu Zhao and Dao-Xiu Zhou.
The EMBO Journal (2023)
Synopsis: DELLA proteins are master repressors of gibberellin (GA) signaling, but the molecular basis of this repression is not well understood. This work shows that one DELLA forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and histone deacetylase HDA702 to repress GA-inducible genes by establishing a silent chromatin state in rice. The rice DELLA protein SLENDER RICE1 (SLR1) interacts with PRC2 and HDA702. SLR1 is required for H3K27 trimethylation (H3K27me3) at a subset of PRC2 targets. GA signaling increases H3K9 acetylation (H3K9ac) and decreases H3K27me3. GA signaling dissociates PRC2 and HDA702 from target genes.
Abstract: "DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling."
Authors: Xu Huang, Hao Tian, Jeongmoo Park, Dong-Ha Oh, Jianhong Hu, Rodolfo Zentella, Hong Qiao, Maheshi Dassanayake and Tai-Ping Sun.
Nature Plants (2023)
Editor's view: Genetic and ChIP–seq analyses of missense DELLA mutants reveal a role of the DELLA PFYRE subdomain in H2A binding, which stabilizes the transcription factor–DELLA–H2A complexes at the target chromatin for global transcription reprogramming.
Abstract: "The DELLA genes, also known as ‘Green Revolution’ genes, encode conserved master growth regulators that control plant development in response to internal and environmental cues. Functioning as nuclear-localized transcription regulators, DELLAs modulate expression of target genes via direct protein–protein interaction of their carboxy-terminal GRAS domain with hundreds of transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here by characterizing new missense alleles of an Arabidopsis DELLA, repressor of ga1-3 (RGA), and co-immunoprecipitation assays, we show that RGA binds histone H2A via the PFYRE subdomain within its GRAS domain to form a TF–RGA–H2A complex at the target chromatin. Chromatin immunoprecipitation followed by sequencing analysis further shows that this activity is essential for RGA association with its target chromatin globally. Our results indicate that, although DELLAs are recruited to target promoters by binding to TFs via the LHR1 subdomain, DELLA–H2A interaction via the PFYRE subdomain is necessary to stabilize the TF–DELLA–H2A complex at the target chromatin. This study provides insights into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants."
Authors: María Florencia Perotti, David Posé and Carmen Martín-Pizarro.
Journal of Experimental Botany (2023)
Abstract: "Fruit ripening involves numerous physiological, structural and metabolic changes that result in the formation of edible fruits. This process is controlled at different molecular levels, with essential roles for phytohormones, transcription factors and epigenetic modifications. Fleshy fruits are classified as either climacteric or non-climacteric species. Climacteric fruits are characterized by a burst in respiration and ethylene production at the onset of ripening, while regulation of non-climacteric fruit ripening has been commonly attributed to abscisic acid (ABA). However, there is controversy as to whether mechanisms regulating fruit ripening are shared between non-climacteric species, and to what extent other hormones contribute alongside ABA. In this review, we summarize classic and recent studies on the accumulation profile and role of ABA and other important hormones in the regulation of non-climacteric fruit development and ripening, as well as their cross-talk, paying special attention to the two main non-climacteric plant models, strawberry and grape. We highlight both the common and different roles of these regulators in these two crops, and discuss the importance of the transcriptional and environmental regulation of fruit ripening, as well as the need to optimize genetic transformation methodologies to facilitate gene functional analyses."
Authors: Junping He, Lu Yao, Lorenzo Pecoraro, Changxiao Liu, Juan Wang, Luqi Huang and Wenyuan Gao.
Critical Reviews in Biotechnology (2023)
Abstract: "Plants make different defense mechanisms in response to different environmental stresses. One common way is to produce secondary metabolites. Temperature is the main environmental factor that regulates plant secondary metabolites, especially flavonoids and terpenoids. Stress caused by temperature decreasing to 4–10 °C is conducive to the accumulation of flavonoids and terpenoids. However, the accumulation mechanism under cold stress still lacks a systematic explanation. In this review, we summarize three aspects of cold stress promoting the accumulation of flavonoids and terpenoids in plants, that is, by affecting (1) the content of endogenous plant hormones, especially jasmonic acid and abscisic acid; (2) the expression level and activity of important transcription factors, such as bHLH and MYB families. This aspect also includes post-translational modification of transcription factors caused by cold stress; (3) key enzyme genes expression and activity in the biosynthesis pathway, in addition, the rate-limiting enzyme and glycosyltransferases genes are responsive to cold stress. The systematic understanding of cold stress regulates flavonoids, and terpenoids will contribute to the future research of genetic engineering breeding, metabolism regulation, glycosyltransferases mining, and plant synthetic biology."
Authors: Chunyu Zhang, Mingyang Jian, Weijun Li, Xiani Yao, Cuirong Tan, Qian Qian, Yilong Hu, Liu Xu and Xingliang Hou.
The Plant Cell (2023)
Abstract: "Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin remodeling SWI/SNF complex that functions in various biological processes by regulating gene expression, is involved in GA signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with each other, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA binding ability of BRM, which promotes the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants."
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Authors: Showkat Ahmad Ganie, Nancy McMulkin and Alessandra Devoto.
Plant, Cell & Environment (2024)
Summary statement: The expression of rice core component circadian clock gene LATE ELONGATED HYPOCOTYL can be induced under salt stress, which alters the expression of Na+ and K+ transporter related genes and genes in the ABA signalling pathway to positively regulate salt stress tolerance in rice.
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."
Authors: Foziya Altaf, Shazia Parveen, Sumira Farooq, Mohammad Lateef Lone, Aehsan Ul Haq and Inayatullah Tahir
Theoretical and Experimental Plant Physiology (2024)
Abstract: "Due to the already strained and severely challenged agricultural ecosystems of the modern world, predicted changes in life cycle of plants, including leaf senescence are receiving significant attention from stakeholders. The onset, progression and terminal phases of leaf senescence are greatly influenced by plant hormones. The senescence of leaves is accelerated by ethylene, jasmonic acid (JA), salicylic acid (SA), abscisic acid (ABA), brassinosteroids and strigolactones (SLs), whereas it is postponed by cytokinins (CKs), gibberellic acid (GA) and auxins. The crosstalk and signal transduction pathways between these growth regulators have been found to regulate leaf senescence by orchestrating various developmental and environmental factors. Premature leaf senescence lessens the plant’s nutritional capacity and shortens the vegetative production schedule, prompting an early transition from the vegetative to the reproductive stage and diminishing crop potential. As a result, a complete understanding of leaf senescence and finding novel ways to delay it is crucial for agricultural productivity. The ability to manipulate leaf senescence for agricultural enhancement has been made possible by significant advances in physiological and molecular awareness of leaf senescence. Although studies pertaining to leaf senescence have been given steadily more attention, there are still numerous challenges that need to be resolved. In this perspective, this review focuses on current advances in understanding the leaf senescence by molecular and genetic analyses with an emphasis on hormonal regulation of leaf senescence. We also hypothesize future research to better comprehend leaf senescence by employing various current technologies."
Authors: Jiří Rudolf, Lucia Tomovičová, Klára Panzarová, Jiří Fajkus, Jan Hejátko and Jan Skalák.
Journal of Experimental Botany (2024)
Abstract: "Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications."
Authors: Yuki Furuta, Haruka Yamamoto, Takeshi Hirakawa, Akira Uemura, Margaret Anne Pelayo, Hideaki Iimura, Naoya Katagiri, Noriko Takeda-Kamiya, Kie Kumaishi, Makoto Shirakawa, Sumie Ishiguro, Yasunori Ichihashi, Takamasa Suzuki, Tatsuaki Goh, Kiminori Toyooka, Toshiro Ito & Nobutoshi Yamaguchi
Nature Communications (2024)
Editor's view: In angiosperms, petal abscission is crucial for reproductive success and seed dispersion. However, the regulation of this abscission remains unclear. Here, the authors identify a process of petal abscission regulated by jasmonic acid via autophagy at the base of Arabidopsis petals.
Abstract: "In angiosperms, the transition from floral-organ maintenance to abscission determines reproductive success and seed dispersion. For petal abscission, cell-fate decisions specifically at the petal-cell base are more important than organ-level senescence or cell death in petals. However, how this transition is regulated remains unclear. Here, we identify a jasmonic acid (JA)-regulated chromatin-state switch at the base of Arabidopsis petals that directs local cell-fate determination via autophagy. During petal maintenance, co-repressors of JA signaling accumulate at the base of petals to block MYC activity, leading to lower levels of ROS. JA acts as an airborne signaling molecule transmitted from stamens to petals, accumulating primarily in petal bases to trigger chromatin remodeling. This allows MYC transcription factors to promote chromatin accessibility for downstream targets, including NAC DOMAIN-CONTAINING PROTEIN102 (ANAC102). ANAC102 accumulates specifically at the petal base prior to abscission and triggers ROS accumulation and cell death via AUTOPHAGY-RELATED GENEs induction. Developmentally induced autophagy at the petal base causes maturation, vacuolar delivery, and breakdown of autophagosomes for terminal cell differentiation. Dynamic changes in vesicles and cytoplasmic components in the vacuole occur in many plants, suggesting JA–NAC-mediated local cell-fate determination by autophagy may be conserved in angiosperms."
Authors: Wei Li, Ying-Chung Jimmy Lin, Ying-Lan Chen, Chenguang Zhou, Shuang Li, Nette De Ridder, Dyoni M. Oliveira, Lanjun Zhang, Baocai Zhang, Jack P. Wang, Changzheng Xu, Xiaokang Fu, Keming Luo, Ai-Min Wu, Taku Demura, Meng-Zhu Lu, Yihua Zhou, Laigeng Li, Toshiaki Umezawa, Wout Boerjan and Vincent L. Chiang.
Molecular Plant (2024)
Abstract: "Cell walls in plants, particularly forest trees, are the major carbon sink of the terrestrial ecosystem. Chemical and biosynthetic features of plant cell walls were revealed early on, focusing mostly on herbaceous model species. Recent developments in genomics, transcriptomics, epigenomics, transgenesis, and associated analytical techniques are enabling novel insights into formation of woody cell walls. Here, we review multilevel regulation of cell wall biosynthesis in forest tree species. We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees. We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage."
Authors: Sampurna Kashyap, Niraj Agarwala and Ramanjulu Sunkar.
Plant Science (2024)
Highlights • Like animals, plants can also memorize past threats and respond robustly to future episodes of the same or similar circumstances. • Stress memory might be generated due to hypersensitive immune responses, epigenetic changes, modulation in hormonal signalling, etc. • The ingenious adaptability of the crop wild relatives (CWRs) in challenging climatic conditions might be due to their peculiar memory functions. • Exploitation of CWRs memory traits may help crop breeders develop more resilient and climate-smart crops. • The ability of plants to modulate root exudation patterns in response to stress conditions can be a component of plant memory.
Abstract: "Being sessile, plants encounter a variety of 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."
Authors: María Florencia Mammarella, Leandro Lucero, Nosheen Hussain, Aitor Muñoz-Lopez, Ying Huang, Lucia Ferrero, Guadalupe L Fernandez-Milmanda, Pablo Manavella, Moussa Benhamed, Martin Crespi, Carlos L. Ballare, José Gutiérrez Marcos, Pilar Cubas and Federico Ariel.
EMBO Journal (2023)
Synopsis: The Arabidopsis lncRNA APOLO influences chromatin architecture to regulate transcription of specific genes, including auxin-responsive genes which are involved in the plant's response to shade avoidance. Here, APOLO is shown to respond to changes in light by influencing transcription and plant behavior. APOLO modulates the expression of BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis, through chromatin looping around the BRC1 promoter. APOLO-mediated chromatin looping is influenced by changes in light exposure and regulates branching behavior. Low-red/far-red light ratio-mediated leaf hyponasty depends on APOLO regulation of auxin-related genes. In vitro-transcribed APOLO directly sprayed onto plants is sufficient to alter plant auxin homeostasis in response to light conditions.
Abstract: "The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA–DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far-red (FR) light, expression of APOLO anti-correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far-red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant–environment interactions may therefore become a new tool for sustainable agriculture."
Authors: Hanqian Feng, Jinjuan Tan and Zhiping Deng.
Journal of Experimental Botany (2023)
Abstract: "Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge about these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators like receptor kinases and transcriptional factors during phytohormone and developmental signaling."
Authors: Sara Zenoni, Stefania Savoi, Nicola Busatto, Giovanni Battista Tornielli and Fabrizio Costa.
Journal of Experimental Botany (2023)
Highlight This review aims to summarize the main transcriptional events coordinating the ripening processes in both climacteric (apple) and non-climacteric (grape) models, focusing on transcription factors and hormonal regulation
Abstract: "Fleshy fruits of angiosperms are organs specialized for promoting seed dispersal by attracting herbivores and enticing them to consume the organ and the contained seeds. Ripening can be broadly defined as the processes serving as a plant strategy to make the fleshy fruit appealing to animals and leads to a coordinated series of changes in color, texture, aroma and flavor, as result of an intricate interplay of genetically and epigenetically programmed events. The ripening of fruits can be categorized into two types: climacteric, which is characterized by a rapid increase in respiration rate typically accompanied by a burst of ethylene production, and non-climacteric, where this pronounced peak in respiration is absent. Here we review the most current knowledge on transcriptomic changes taking place in apple (climacteric) and grapevine (non-climacteric) fruit during ripening, with the aim to highlight specific and common hormonal and molecular events governing the process in both species. In this perspective, we found that specific NAC transcription factor members participate in the ripening initiation in grape and are involved in the attempt to restore the normal physiological ripening progression in impaired fruit ripening physiology in apple. These elements suggest the existence of a common regulatory mechanism operated by NAC transcription factors and auxin in the two species."
Authors: Barbara Wójcikowska, Samia Belaidi and Hélène S. Robert.
Journal of Experimental Botany (2023)
Abstract: "For many years, research has been carried out to understand the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is understanding the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on the MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review paper summarizes over thirty years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, i.e., embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin-dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and finally, the list of genes under its direct control. In addition, the information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years."
Authors: Liqun Tang, Huimei Wang, Guanghao Li, Juan Zhao, Zhiyong Li, Xixi Liu, Yazhou Shu, Wanning Liu, Shuang Wang, Jie Huang, Jiezheng Ying, Xiaohong Tong, Wenya Yuan, Xiangjin Wei, Shaoqing Tang, Yifeng Wang, Qingyun Bu and Jian Zhang.
Journal of Advanced Research (2024)
Highlights • ABF1 is induced by ABA and promotes ABA repression on rice flowering. • SAPK8 phosphorylates ABF1 and strengthens the latter participating in ABA-mediated flowering inhibition. • ABA enhances the direct transcriptional repression of ABF1 on Ehd1 and Ehd2. • ABF1 recruits PRC2 complex to deposit H3K27me3 to suppress Ehd1 and Ehd2.
Abstract: "Introduction - Rice flowering is a major agronomic trait, determining yield and ecological adaptability in particular regions. ABA plays an essential role in rice flowering, but the underlying molecular mechanism remains largely elusive. Objectives - In this study, we demonstrated a “SAPK8-ABF1-Ehd1/Ehd2” pathway, through which exogenous ABA represses rice flowering in a photoperiod-independent manner. Methods - We generated abf1 and sapk8 mutants using the CRISPR-Cas9 method. Using yeast two-hybrid, Pull down, BiFC and kinase assays, SAPK8 interacted and phosphorylated ABF1. ABF1 directly bound to the promoters of Ehd1 and Ehd2 using ChIP-qPCR, EMSA, and LUC transient transcriptional activity assay, and suppressed the transcription of these genes. Results - Under both long day and short day conditions, simultaneous knock-out of ABF1 and its homolog bZIP40 accelerated flowering, while SAPK8 and ABF1 over-expression lines exhibited delayed flowering and hypersensitivity to ABA-mediated flowering repression. After perceiving the ABA signal, SAPK8 physically binds to and phosphorylates ABF1 to enhance its binding to the promoters of master positive flowering regulators Ehd1 and Ehd2. Upon interacting with FIE2, ABF1 recruited PRC2 complex to deposit H3K27me3 suppressive histone modification on Ehd1 and Ehd2 to suppress these genes transcription, thereby leading to later flowering. Conclusion - Our work highlighted the biological functions of SAPK8 and ABF1 in ABA signaling, flowering control and the involvement of a PRC2-mediated epigenetic repression mechanism in the transcription regulation governed by ABF1 on ABA-mediated rice flowering repression."
Authors: Jingni Wu, Xiao Mei, Jinyu Zhang, Luhuan Ye, Yezhou Hu, Tao Chen, Yiping Wang, Menghui Liu, Yijing Zhang and Xiu-Fang Xin.
Plant Physiology (2023)
Abstract: "The apoplast of plant leaves, the intercellular space between mesophyll cells, is normally largely filled with air with a minimal amount of liquid water in it, which is essential for key physiological processes such as gas exchange to occur. Phytopathogens exploit virulence factors to induce a water-rich environment, or “water-soaked” area, in the apoplast of the infected leaf tissue to promote disease. We propose that plants evolved a “water soaking” pathway, which normally keeps a non-flooded leaf apoplast for plant growth but is disturbed by microbial pathogens to facilitate infection. Investigation of the “water soaking” pathway and leaf water control mechanisms is a fundamental, yet previously-overlooked, aspect of plant physiology. To identify key components in the “water soaking” pathway, we performed a genetic screen to isolate Arabidopsis (Arabidopsis thaliana) severe water soaking (sws) mutants that show liquid water over-accumulation in the leaf under high air humidity, a condition required for visible water soaking. Here we report the sws1 mutant, which displays rapid water soaking upon high humidity treatment due to a loss-of-function mutation in CURLY LEAF (CLF), encoding a histone methyl-transferase in the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2). We found that the sws1 (clf) mutant exhibits enhanced abscisic acid (ABA) levels and stomatal closure, which are indispensable for its water soaking phenotype and mediated by CLF’s epigenetic regulation of a group of ABA-associated NAM, ATAF and CUC (NAC) transcription factor genes, NAC019/055/072. The clf mutant showed weakened immunity, which likely also contributes to the water soaking phenotype. In addition, the clf plant supports a substantially higher level of Pseudomonas syringae pathogen-induced water soaking and bacterial multiplication, in an ABA pathway and NAC019/055/072-dependent manner. Collectively, our study sheds light on an important question in plant biology and demonstrates CLF as a key modulator of leaf liquid water status via epigenetic regulation of the ABA pathway and stomatal movement."
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