Shiqi Wen, Hongju Jian, Lina Shang, Philip James Kear, Meihua Zhang, Yan Li, Pingping Yuan, Dianqiu Lyu
Drought and high salt stress have a great negative impact on potato growth and development. However, the molecular mechanisms by which different tissues and organs of potato plants respond to drought and high salt stress at different stress times lack definition. In this study, we mapped the whole genome of THSs in potato in response to different stresses using RNA-seq and ATAC-seq technologies and constructed the unique and shared transcriptional regulatory networks (TRNs) under different stresses, stress time points, and tissues in potato. The results showed opposite trends for changes in chromatin accessibility and expression of genes under drought and salt stresses. Forty-eight hours and root-specific TRNs were more complex than those of 3 h and leaf, and there were genes with inconsistent drought- and salt-stress-regulated expression only in root-shared TRNs, demonstrating the variability of potato's response to stresses under different tissues and treatment times. These results provide a basis for elucidating the transcriptional mechanisms underlying the specific response of potato to drought or salt stress and the common response to salt and drought stress.
{"title":"Comprehensive transcriptional regulatory networks in potato through chromatin accessibility and transcriptome under drought and salt stresses","authors":"Shiqi Wen, Hongju Jian, Lina Shang, Philip James Kear, Meihua Zhang, Yan Li, Pingping Yuan, Dianqiu Lyu","doi":"10.1111/tpj.70081","DOIUrl":"https://doi.org/10.1111/tpj.70081","url":null,"abstract":"<div>\u0000 \u0000 <p>Drought and high salt stress have a great negative impact on potato growth and development. However, the molecular mechanisms by which different tissues and organs of potato plants respond to drought and high salt stress at different stress times lack definition. In this study, we mapped the whole genome of THSs in potato in response to different stresses using RNA-seq and ATAC-seq technologies and constructed the unique and shared transcriptional regulatory networks (TRNs) under different stresses, stress time points, and tissues in potato. The results showed opposite trends for changes in chromatin accessibility and expression of genes under drought and salt stresses. Forty-eight hours and root-specific TRNs were more complex than those of 3 h and leaf, and there were genes with inconsistent drought- and salt-stress-regulated expression only in root-shared TRNs, demonstrating the variability of potato's response to stresses under different tissues and treatment times. These results provide a basis for elucidating the transcriptional mechanisms underlying the specific response of potato to drought or salt stress and the common response to salt and drought stress.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Saline-alkali stress has detrimental effects on growth and development of rice (Oryza sativa L.). Domesticated rice cultivars with high saline-alkali tolerance (SAT) are essential for sustainable agriculture. To explore the genomic basis underlying SAT in rice, we integrate genome-wide association study (GWAS) with selective sweep analysis using a core population consisting of 234 cultivars grown in the saline and normal fields across three consecutive years and identify 70 genes associated with SAT with signals of selection and evolution between subpopulations of tolerance and sensitivity. We detected and subsequently characterized GATA19 trans-regulated SAT1/OsCYL4 that regulated SAT through reactive oxygen species (ROS) scavenging pathway. Our results provide a comprehensive insight into genome-wide natural variants and selection sweep underlying saline-alkali tolerance and pave avenues for SAT breeding through genome editing and genomic selection in rice.
{"title":"Genome-wide association and selection studies reveal genomic insight into saline-alkali tolerance in rice","authors":"Jin Li, Chen Xu, Yunlu Tian, Gaoming Chen, Wenchao Chi, Zhaoyang Dai, Jing Li, Chunyuan Wang, Xinran Cheng, Yan Liu, Zhiguang Sun, Jingfang Li, Baoxiang Wang, Dayong Xu, Xianjun Sun, Hui Zhang, Chengsong Zhu, Chunming Wang, Jianmin Wan","doi":"10.1111/tpj.70056","DOIUrl":"https://doi.org/10.1111/tpj.70056","url":null,"abstract":"<div>\u0000 \u0000 <p>Saline-alkali stress has detrimental effects on growth and development of rice (<i>Oryza sativa</i> L.). Domesticated rice cultivars with high saline-alkali tolerance (SAT) are essential for sustainable agriculture. To explore the genomic basis underlying SAT in rice, we integrate genome-wide association study (GWAS) with selective sweep analysis using a core population consisting of 234 cultivars grown in the saline and normal fields across three consecutive years and identify 70 genes associated with SAT with signals of selection and evolution between subpopulations of tolerance and sensitivity. We detected and subsequently characterized GATA19 trans-regulated <i>SAT1/OsCYL4</i> that regulated SAT through reactive oxygen species (ROS) scavenging pathway. Our results provide a comprehensive insight into genome-wide natural variants and selection sweep underlying saline-alkali tolerance and pave avenues for SAT breeding through genome editing and genomic selection in rice.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Heat stress impacts all aspects of life, from evolution to global food security. Therefore, it becomes essential to understand how plants respond to heat stress, especially in the context of climate change. The heat stress response (HSR) involves three main components: sensing, signal transduction, and cellular reprogramming. Here, I focus on the heat stress sensing component. How can cells detect heat stress if it is not a signalling particle? To answer this question, I have looked at the molecular definition of heat stress. It can be defined as any particular rise in the optimum growth temperature that leads to higher-than-normal levels of reactive molecular species and macromolecular damage to biological membranes, proteins, and nucleic acid polymers (DNA and RNA). It is precisely these stress-specific alterations that are detected by heat stress sensors, upon which they would immediately trigger the appropriate level of the HSR. In addition, the work towards thermotolerance is complemented by a second type of response, here called the cellular homeostasis response (CHR). Upon mild and extreme temperature changes, the CHR is triggered by plant thermosensors, which are responsible for monitoring temperature information. Heat stress sensors and thermosensors are distinct types of molecules, each with unique modes of activation and functions. While many recent reviews provide a comprehensive overview of plant thermosensors, there remains a notable gap in the review literature regarding an in-depth analysis of plant heat stress sensors. Here, I attempt to summarise our current knowledge of the cellular sensors involved in triggering the plant HSR.
{"title":"Molecular aspects of heat stress sensing in land plants","authors":"Cristiane Paula Gomes Calixto","doi":"10.1111/tpj.70069","DOIUrl":"https://doi.org/10.1111/tpj.70069","url":null,"abstract":"<p>Heat stress impacts all aspects of life, from evolution to global food security. Therefore, it becomes essential to understand how plants respond to heat stress, especially in the context of climate change. The heat stress response (HSR) involves three main components: sensing, signal transduction, and cellular reprogramming. Here, I focus on the heat stress sensing component. How can cells detect heat stress if it is not a signalling particle? To answer this question, I have looked at the molecular definition of heat stress. It can be defined as any particular rise in the optimum growth temperature that leads to higher-than-normal levels of reactive molecular species and macromolecular damage to biological membranes, proteins, and nucleic acid polymers (DNA and RNA). It is precisely these stress-specific alterations that are detected by heat stress sensors, upon which they would immediately trigger the appropriate level of the HSR. In addition, the work towards thermotolerance is complemented by a second type of response, here called the cellular homeostasis response (CHR). Upon mild and extreme temperature changes, the CHR is triggered by plant thermosensors, which are responsible for monitoring temperature information. Heat stress sensors and thermosensors are distinct types of molecules, each with unique modes of activation and functions. While many recent reviews provide a comprehensive overview of plant thermosensors, there remains a notable gap in the review literature regarding an in-depth analysis of plant heat stress sensors. Here, I attempt to summarise our current knowledge of the cellular sensors involved in triggering the plant HSR.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Branching is the main factor that determines plant architecture and is closely related to plant adaptation to the environment. Cold stress can inhibit lateral bud elongation in plants, but the underlying mechanism is still unclear. Here, we report that the cold stress-induced bZIP family transcription factor CmbZIP19 inhibits lateral bud elongation in chrysanthemum. We identified the target gene of CmbZIP19 as the brassinolide (BR) synthesis-related gene CmDWF1 by integrating RNA-seq and DAP-seq data. CmbZIP19 can directly bind to the ZDRE-like motif in the promoter region of CmDWF1, thereby inhibiting the expression of CmDWF1. We confirmed that CmDWF1 can promote the lateral branch elongation of chrysanthemum by genetic transformation. The branching phenotype of CmbZIP19-RNAi plants could be restituted by BR treatment. Taken together, the results suggest that CmbZIP19 modulates plant architecture by suppressing BR synthesis.
{"title":"CmbZIP19 inhibits lateral bud elongation via the brassinolide pathway in chrysanthemum","authors":"Lingling Zhang, Xianrong Fu, Jingxuan Ye, Shaocong Chen, Jinyu Jin, Weixin Liu, Zhaohe Zhang, Lijie Zhou, Sumei Chen, Weimin Fang, Aiping Song, Fadi Chen","doi":"10.1111/tpj.70080","DOIUrl":"https://doi.org/10.1111/tpj.70080","url":null,"abstract":"<div>\u0000 \u0000 <p>Branching is the main factor that determines plant architecture and is closely related to plant adaptation to the environment. Cold stress can inhibit lateral bud elongation in plants, but the underlying mechanism is still unclear. Here, we report that the cold stress-induced bZIP family transcription factor CmbZIP19 inhibits lateral bud elongation in chrysanthemum. We identified the target gene of CmbZIP19 as the brassinolide (BR) synthesis-related gene <i>CmDWF1</i> by integrating RNA-seq and DAP-seq data. CmbZIP19 can directly bind to the ZDRE-like motif in the promoter region of <i>CmDWF1</i>, thereby inhibiting the expression of <i>CmDWF1</i>. We confirmed that CmDWF1 can promote the lateral branch elongation of chrysanthemum by genetic transformation. The branching phenotype of CmbZIP19-RNAi plants could be restituted by BR treatment. Taken together, the results suggest that CmbZIP19 modulates plant architecture by suppressing BR synthesis.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jun Zhang, Rui Chen, Fan Dai, Yue Tian, Yue Shi, Ying He, Yan Hu, Tianzhen Zhang
Recent advances in single-cell transcriptomics have greatly expanded our knowledge of plant development and cellular responses. However, analyzing fiber cell differentiation in plants, particularly in cotton, remains a complex challenge. A spatial transcriptomic map of ovule from −1 DPA, 0 DPA, and 1 DPA in cotton was successfully constructed, which helps to explain the important role of sucrose synthesis and lipid metabolism during early fiber development. Additionally, single-cell RNA sequencing (scRNA-seq) further highlighted the cellular heterogeneity and identified clusters of fiber developmental marker genes. Integration of spatial and scRNA-seq data unveiled key genes SVB and SVBL involved in fiber initiation, suggesting functional redundancy between them. These findings provide a detailed molecular landscape of cotton fiber development, offering valuable insights for enhancing lint yield.
{"title":"Spatial transcriptome and single-cell RNA sequencing reveal the molecular basis of cotton fiber initiation development","authors":"Jun Zhang, Rui Chen, Fan Dai, Yue Tian, Yue Shi, Ying He, Yan Hu, Tianzhen Zhang","doi":"10.1111/tpj.70064","DOIUrl":"https://doi.org/10.1111/tpj.70064","url":null,"abstract":"<div>\u0000 \u0000 <p>Recent advances in single-cell transcriptomics have greatly expanded our knowledge of plant development and cellular responses. However, analyzing fiber cell differentiation in plants, particularly in cotton, remains a complex challenge. A spatial transcriptomic map of ovule from −1 DPA, 0 DPA, and 1 DPA in cotton was successfully constructed, which helps to explain the important role of sucrose synthesis and lipid metabolism during early fiber development. Additionally, single-cell RNA sequencing (scRNA-seq) further highlighted the cellular heterogeneity and identified clusters of fiber developmental marker genes. Integration of spatial and scRNA-seq data unveiled key genes <i>SVB</i> and <i>SVBL</i> involved in fiber initiation, suggesting functional redundancy between them. These findings provide a detailed molecular landscape of cotton fiber development, offering valuable insights for enhancing lint yield.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>Developmental processes and responses to environmental stimuli are governed by plant-specific signals, such as peptides of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family (Cock & McCormick, <span>2001</span>). They are involved in processes like stomata closure, vascular development, and meristem homeostasis (reviewed in Fletcher, <span>2020</span>). The CLE signaling pathway is one such pathway; it maintains the stem cell population in the shoot apical meristem in Arabidopsis. The homeobox transcription factor WUSCHEL (WUS) is expressed in cells of the meristem organizing center, then moves to stem cells in the outer layers of the meristem, where it activates the expression of the CLE peptide CLV3 (Carles & Fletcher, <span>2003</span>). The mature peptide is secreted and binds to the extracellular leucine-rich repeats of receptor-like kinase CLV1, triggering a signal cascade that represses <i>WUS</i> expression in the organizing center. A similar pathway also regulates shoot meristem homeostasis of other plants (e.g., Je et al., <span>2016</span>; Suzaki et al., <span>2008</span>).</p><p>CLE peptides are found across all land plant lineages, but they are absent in algae, suggesting that CLEs likely evolved in the last common ancestor of land plants (Whitewoods, <span>2021</span>). However, while bryophyte genomes have both <i>WUS</i> and <i>CLE</i> genes, the genes function in separate processes (Hirakawa et al., <span>2020</span>). Therefore, the prevalent hypothesis is that WOX-CLE signaling evolved after the divergence of bryophytes (Whitewoods, <span>2021</span>). Kelley Renninger, first author of the highlighted publication and then a PhD student in Chi-Lien Cheng's group at the University of Iowa, decided to address the question of how and when WOX transcription factors were integrated into CLE-receptor signaling pathways during the evolution of land plants.</p><p>As ferns represent an evolutionary intermediate between bryophytes and flowering plants, the authors decided to use <i>Ceratopteris richardii</i>, a homosporous fern, for their study. Its mature sporophyte produces haploid spores, which germinate and grow into multicellular hermaphrodite or male gametophytes. Male gametophytes produce multiple antheridia that produce sperm. The hermaphrodite gametophyte develops one multicellular meristem, called the marginal meristem, and next to the meristem notch, the egg-bearing archegonia initiate (Figure 1a) (Geng et al., <span>2022</span>). The <i>Ceratopteris</i> genome has five <i>WOX</i> genes (Nardmann & Werr, <span>2012</span>) and CLE peptides, but the sequences encoding CLE peptides and their functions are unknown.</p><p>Based on BLASTp searches with the CLEs of Arabidopsis and those of the ferns <i>Azolla filiculoides</i> and <i>Salvinia cucullata</i>, the authors identified 11 loci in the <i>Ceratopteris</i> genome encoding CLEs. The C-terminal CLE motif represents the mature peptide. The CLE motif of CrCLV3 was
{"title":"Fern-tastic discoveries: CLAVATA3 and WOX signaling pathways in fern gametophyte development","authors":"Gwendolyn K. Kirschner","doi":"10.1111/tpj.70093","DOIUrl":"https://doi.org/10.1111/tpj.70093","url":null,"abstract":"<p>Developmental processes and responses to environmental stimuli are governed by plant-specific signals, such as peptides of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family (Cock & McCormick, <span>2001</span>). They are involved in processes like stomata closure, vascular development, and meristem homeostasis (reviewed in Fletcher, <span>2020</span>). The CLE signaling pathway is one such pathway; it maintains the stem cell population in the shoot apical meristem in Arabidopsis. The homeobox transcription factor WUSCHEL (WUS) is expressed in cells of the meristem organizing center, then moves to stem cells in the outer layers of the meristem, where it activates the expression of the CLE peptide CLV3 (Carles & Fletcher, <span>2003</span>). The mature peptide is secreted and binds to the extracellular leucine-rich repeats of receptor-like kinase CLV1, triggering a signal cascade that represses <i>WUS</i> expression in the organizing center. A similar pathway also regulates shoot meristem homeostasis of other plants (e.g., Je et al., <span>2016</span>; Suzaki et al., <span>2008</span>).</p><p>CLE peptides are found across all land plant lineages, but they are absent in algae, suggesting that CLEs likely evolved in the last common ancestor of land plants (Whitewoods, <span>2021</span>). However, while bryophyte genomes have both <i>WUS</i> and <i>CLE</i> genes, the genes function in separate processes (Hirakawa et al., <span>2020</span>). Therefore, the prevalent hypothesis is that WOX-CLE signaling evolved after the divergence of bryophytes (Whitewoods, <span>2021</span>). Kelley Renninger, first author of the highlighted publication and then a PhD student in Chi-Lien Cheng's group at the University of Iowa, decided to address the question of how and when WOX transcription factors were integrated into CLE-receptor signaling pathways during the evolution of land plants.</p><p>As ferns represent an evolutionary intermediate between bryophytes and flowering plants, the authors decided to use <i>Ceratopteris richardii</i>, a homosporous fern, for their study. Its mature sporophyte produces haploid spores, which germinate and grow into multicellular hermaphrodite or male gametophytes. Male gametophytes produce multiple antheridia that produce sperm. The hermaphrodite gametophyte develops one multicellular meristem, called the marginal meristem, and next to the meristem notch, the egg-bearing archegonia initiate (Figure 1a) (Geng et al., <span>2022</span>). The <i>Ceratopteris</i> genome has five <i>WOX</i> genes (Nardmann & Werr, <span>2012</span>) and CLE peptides, but the sequences encoding CLE peptides and their functions are unknown.</p><p>Based on BLASTp searches with the CLEs of Arabidopsis and those of the ferns <i>Azolla filiculoides</i> and <i>Salvinia cucullata</i>, the authors identified 11 loci in the <i>Ceratopteris</i> genome encoding CLEs. The C-terminal CLE motif represents the mature peptide. The CLE motif of CrCLV3 was","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70093","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yasutomo Hoshika, Elena Paoletti, Claudia Pisuttu, Lorenzo Cotrozzi, Matthew Haworth, Elisa Pellegrini, Cristina Nali, Rafael Vasconcelos Ribeiro, Juliana Lischka Sampaio Mayer, Barbara Baesso Moura
Tropospheric ozone (O3) is a phytotoxic air pollutant that impairs photosynthesis. The mechanisms of O3-induced reduction of mesophyll conductance (gm) are not clear. We investigated the interaction of O3 and leaf age on gm by using structural equation modelling (SEM) for two poplar clones (I-214 and Oxford) exposed to three O3 levels (ambient air, AA; 1.5 × AA; 2.0 × AA) in a free-air controlled experiment. Clone-specific phenological responses to elevated O3 were found: I-214 showed a rapid leaf turnover and formed new productive leaves, whereas Oxford was more ‘conservative’ maintaining old or injured leaves. In the I-214 clone with fast leaf turnover, gm was reduced due to increasing cell wall thickness in new leaves, a possible reaction to increase its resistance against O3 damage. As I-214 leaves aged, a decrease in the fraction of the mesophyll surface area unoccupied by chloroplasts was observed at 2.0 × AA prior to a reduction in photosynthesis. In the Oxford clone with slow leaf turnover, gm was mainly affected by physiological rather than structural factors: in particular, a marked reduction of gm caused by abscisic acid (ABA) was noticed. As photosynthesis is limited by diffusional barriers, O3 effects on gm will be key for carbon sequestration modelling of O3 pollution and climate change.
{"title":"Leaf phenology determines the response of poplar genotypes to O3 through mesophyll conductance","authors":"Yasutomo Hoshika, Elena Paoletti, Claudia Pisuttu, Lorenzo Cotrozzi, Matthew Haworth, Elisa Pellegrini, Cristina Nali, Rafael Vasconcelos Ribeiro, Juliana Lischka Sampaio Mayer, Barbara Baesso Moura","doi":"10.1111/tpj.70091","DOIUrl":"https://doi.org/10.1111/tpj.70091","url":null,"abstract":"<p>Tropospheric ozone (O<sub>3</sub>) is a phytotoxic air pollutant that impairs photosynthesis. The mechanisms of O<sub>3</sub>-induced reduction of mesophyll conductance (<i>g</i><sub>m</sub>) are not clear. We investigated the interaction of O<sub>3</sub> and leaf age on <i>g</i><sub>m</sub> by using structural equation modelling (SEM) for two poplar clones (I-214 and Oxford) exposed to three O<sub>3</sub> levels (ambient air, AA; 1.5 × AA; 2.0 × AA) in a free-air controlled experiment. Clone-specific phenological responses to elevated O<sub>3</sub> were found: I-214 showed a rapid leaf turnover and formed new productive leaves, whereas Oxford was more ‘conservative’ maintaining old or injured leaves. In the I-214 clone with fast leaf turnover, <i>g</i><sub>m</sub> was reduced due to increasing cell wall thickness in new leaves, a possible reaction to increase its resistance against O<sub>3</sub> damage. As I-214 leaves aged, a decrease in the fraction of the mesophyll surface area unoccupied by chloroplasts was observed at 2.0 × AA prior to a reduction in photosynthesis. In the Oxford clone with slow leaf turnover, <i>g</i><sub>m</sub> was mainly affected by physiological rather than structural factors: in particular, a marked reduction of <i>g</i><sub>m</sub> caused by abscisic acid (ABA) was noticed. As photosynthesis is limited by diffusional barriers, O<sub>3</sub> effects on <i>g</i><sub>m</sub> will be key for carbon sequestration modelling of O<sub>3</sub> pollution and climate change.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70091","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tito Damiani, Joshua Smith, Téo Hebra, Milana Perković, Marijo Čičak, Alžběta Kadlecová, Vlastimil Rybka, Martin Dračínský, Tomáš Pluskal
Plant specialized metabolites play key roles in diverse physiological processes and ecological interactions. Identifying structurally novel metabolites, as well as discovering known compounds in new species, is often crucial for answering broader biological questions. The Piper genus (Piperaceae family) is known for its special phytochemistry and has been extensively studied over the past decades. Here, we investigated the alkaloid diversity of Piper fimbriulatum, a myrmecophytic plant native to Central America, using a metabolomics workflow that combines untargeted LC–MS/MS analysis with a range of recently developed computational tools. Specifically, we leverage open MS/MS spectral libraries and metabolomics data repositories for metabolite annotation, guiding isolation efforts toward structurally new compounds (i.e., dereplication). As a result, we identified several alkaloids belonging to five different classes and isolated one novel seco-benzylisoquinoline alkaloid featuring a linear quaternary amine moiety which we named fimbriulatumine. Notably, many of the identified compounds were never reported in Piperaceae plants. Our findings expand the known alkaloid diversity of this family and demonstrate the value of revisiting well-studied plant families using state-of-the-art computational metabolomics workflows to uncover previously overlooked chemodiversity. To contextualize our findings within a broader biological context, we employed a workflow for automated mining of literature reports of the identified alkaloid scaffolds and mapped the results onto the angiosperm tree of life. By doing so, we highlight the remarkable alkaloid diversity within the Piper genus and provide a framework for generating hypotheses on the biosynthetic evolution of these specialized metabolites. Many of the computational tools and data resources used in this study remain underutilized within the plant science community. This manuscript demonstrates their potential through a practical application and aims to promote broader accessibility to untargeted metabolomics approaches.
{"title":"Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum","authors":"Tito Damiani, Joshua Smith, Téo Hebra, Milana Perković, Marijo Čičak, Alžběta Kadlecová, Vlastimil Rybka, Martin Dračínský, Tomáš Pluskal","doi":"10.1111/tpj.70086","DOIUrl":"https://doi.org/10.1111/tpj.70086","url":null,"abstract":"<p>Plant specialized metabolites play key roles in diverse physiological processes and ecological interactions. Identifying structurally novel metabolites, as well as discovering known compounds in new species, is often crucial for answering broader biological questions. The <i>Piper</i> genus (<i>Piperaceae</i> family) is known for its special phytochemistry and has been extensively studied over the past decades. Here, we investigated the alkaloid diversity of <i>Piper fimbriulatum</i>, a myrmecophytic plant native to Central America, using a metabolomics workflow that combines untargeted LC–MS/MS analysis with a range of recently developed computational tools. Specifically, we leverage open MS/MS spectral libraries and metabolomics data repositories for metabolite annotation, guiding isolation efforts toward structurally new compounds (i.e., dereplication). As a result, we identified several alkaloids belonging to five different classes and isolated one novel <i>seco</i>-benzylisoquinoline alkaloid featuring a linear quaternary amine moiety which we named fimbriulatumine. Notably, many of the identified compounds were never reported in Piperaceae plants. Our findings expand the known alkaloid diversity of this family and demonstrate the value of revisiting well-studied plant families using state-of-the-art computational metabolomics workflows to uncover previously overlooked chemodiversity. To contextualize our findings within a broader biological context, we employed a workflow for automated mining of literature reports of the identified alkaloid scaffolds and mapped the results onto the angiosperm tree of life. By doing so, we highlight the remarkable alkaloid diversity within the <i>Piper</i> genus and provide a framework for generating hypotheses on the biosynthetic evolution of these specialized metabolites. Many of the computational tools and data resources used in this study remain underutilized within the plant science community. This manuscript demonstrates their potential through a practical application and aims to promote broader accessibility to untargeted metabolomics approaches.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70086","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Athen N. Kimberlin, Sakil Mahmud, Rebekah E. Holtsclaw, Alexie Walker, Kristyn Conrad, Stewart A. Morley, Ruth Welti, Doug K. Allen, Abraham J. Koo
Bioengineering efforts to increase oil in non-storage vegetative tissues, which constitute the majority of plant biomass, are promising sustainable sources of renewable fuels and feedstocks. While plants typically do not accumulate significant amounts of triacylglycerol (TAG) in vegetative tissues, we report here that the expression of a plastid-localized phospholipase A1 protein, DEFECTIVE IN ANTHER DEHISCENCE1 (DAD1), led to a substantial increase in leaf TAG in Arabidopsis. Using an inducible system to control DAD1 expression circumvented growth penalties associated with overexpressing DAD1 and resulted in a rapid burst of TAG within several hours. The increase of TAG was accompanied by the formation of oil bodies in the leaves, petioles, and stems, but not in the roots. Lipid analysis indicated that the increase in TAG was negatively correlated with plastidial galactolipid concentration. The fatty acid (FA) composition of TAG predominantly consisted of 18:3. Expression of DAD1 in the fad3fad7fad8 mutant, devoid of 18:3, resulted in comparable TAG accumulation with 18:2 as the major FA constituent, reflecting the flexible in vivo substrate use of DAD1. The transient expression of either Arabidopsis DAD1 or Nicotiana benthamiana DAD1 (NbDAD1) in N. benthamiana leaves stimulated the accumulation of TAG. Similarly, transgenic soybeans expressing Arabidopsis DAD1 exhibited an accumulation of TAG in the leaves, showcasing the biotechnological potential of this technology. In summary, inducible expression of a plastidial lipase resulted in enhanced oil production in vegetative tissues, extending our understanding of lipid remodeling mediated by DAD1 and offering a valuable tool for metabolic engineering.
{"title":"Inducible expression of DEFECTIVE IN ANTHER DEHISCENCE 1 enhances triacylglycerol accumulation and lipid droplet formation in vegetative tissues","authors":"Athen N. Kimberlin, Sakil Mahmud, Rebekah E. Holtsclaw, Alexie Walker, Kristyn Conrad, Stewart A. Morley, Ruth Welti, Doug K. Allen, Abraham J. Koo","doi":"10.1111/tpj.70088","DOIUrl":"https://doi.org/10.1111/tpj.70088","url":null,"abstract":"<p>Bioengineering efforts to increase oil in non-storage vegetative tissues, which constitute the majority of plant biomass, are promising sustainable sources of renewable fuels and feedstocks. While plants typically do not accumulate significant amounts of triacylglycerol (TAG) in vegetative tissues, we report here that the expression of a plastid-localized phospholipase A1 protein, DEFECTIVE IN ANTHER DEHISCENCE1 (DAD1), led to a substantial increase in leaf TAG in Arabidopsis. Using an inducible system to control DAD1 expression circumvented growth penalties associated with overexpressing DAD1 and resulted in a rapid burst of TAG within several hours. The increase of TAG was accompanied by the formation of oil bodies in the leaves, petioles, and stems, but not in the roots. Lipid analysis indicated that the increase in TAG was negatively correlated with plastidial galactolipid concentration. The fatty acid (FA) composition of TAG predominantly consisted of 18:3. Expression of DAD1 in the <i>fad3fad7fad8</i> mutant, devoid of 18:3, resulted in comparable TAG accumulation with 18:2 as the major FA constituent, reflecting the flexible <i>in vivo</i> substrate use of DAD1. The transient expression of either Arabidopsis DAD1 or <i>Nicotiana benthamiana</i> DAD1 (NbDAD1) in <i>N. benthamiana</i> leaves stimulated the accumulation of TAG. Similarly, transgenic soybeans expressing Arabidopsis DAD1 exhibited an accumulation of TAG in the leaves, showcasing the biotechnological potential of this technology. In summary, inducible expression of a plastidial lipase resulted in enhanced oil production in vegetative tissues, extending our understanding of lipid remodeling mediated by DAD1 and offering a valuable tool for metabolic engineering.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sugarcane, which provides 80% of global table sugar and 40% of biofuel, presents unique breeding challenges due to its highly polyploid, heterozygous, and frequently aneuploid genome. Significant progress has been made in developing genetic resources, including the recently completed reference genome of the sugarcane cultivar R570 and pan-genomic resources from sorghum, a closely related diploid species. Biotechnological approaches including RNA interference (RNAi), overexpression of transgenes, and gene editing technologies offer promising avenues for accelerating sugarcane improvement. These methods have successfully targeted genes involved in important traits such as sucrose accumulation, lignin biosynthesis, biomass oil accumulation, and stress response. One of the main transformation methods—biolistic gene transfer or Agrobacterium-mediated transformation—coupled with efficient tissue culture protocols, is typically used for implementing these biotechnology approaches. Emerging technologies show promise for overcoming current limitations. The use of morphogenic genes can help address genotype constraints and improve transformation efficiency. Tissue culture-free technologies, such as spray-induced gene silencing, virus-induced gene silencing, or virus-induced gene editing, offer potential for accelerating functional genomics studies. Additionally, novel approaches including base and prime editing, orthogonal synthetic transcription factors, and synthetic directed evolution present opportunities for enhancing sugarcane traits. These advances collectively aim to improve sugarcane's efficiency as a crop for both sugar and biofuel production. This review aims to discuss the progress made in sugarcane methodologies, with a focus on RNAi and gene editing approaches, how RNAi can be used to inform functional gene targets, and future improvements and applications.
{"title":"RNAi and genome editing of sugarcane: Progress and prospects","authors":"Eleanor Brant, Evelyn Zuniga-Soto, Fredy Altpeter","doi":"10.1111/tpj.70048","DOIUrl":"https://doi.org/10.1111/tpj.70048","url":null,"abstract":"<p>Sugarcane, which provides 80% of global table sugar and 40% of biofuel, presents unique breeding challenges due to its highly polyploid, heterozygous, and frequently aneuploid genome. Significant progress has been made in developing genetic resources, including the recently completed reference genome of the sugarcane cultivar R570 and pan-genomic resources from sorghum, a closely related diploid species. Biotechnological approaches including RNA interference (RNAi), overexpression of transgenes, and gene editing technologies offer promising avenues for accelerating sugarcane improvement. These methods have successfully targeted genes involved in important traits such as sucrose accumulation, lignin biosynthesis, biomass oil accumulation, and stress response. One of the main transformation methods—biolistic gene transfer or <i>Agrobacterium</i>-mediated transformation—coupled with efficient tissue culture protocols, is typically used for implementing these biotechnology approaches. Emerging technologies show promise for overcoming current limitations. The use of morphogenic genes can help address genotype constraints and improve transformation efficiency. Tissue culture-free technologies, such as spray-induced gene silencing, virus-induced gene silencing, or virus-induced gene editing, offer potential for accelerating functional genomics studies. Additionally, novel approaches including base and prime editing, orthogonal synthetic transcription factors, and synthetic directed evolution present opportunities for enhancing sugarcane traits. These advances collectively aim to improve sugarcane's efficiency as a crop for both sugar and biofuel production. This review aims to discuss the progress made in sugarcane methodologies, with a focus on RNAi and gene editing approaches, how RNAi can be used to inform functional gene targets, and future improvements and applications.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}