{"title":"Bryophyte ELIPs as Evolutionary Guardians: Engineering Chloroplast Resilience and ABA-Enhanced Drought Tolerance in Crops.","authors":"Qinqin Niu, Luyi Zhao, Yuxi Dang, Ruoyi Guo, Ke Deng, Lihong Xiao","doi":"10.1111/pce.70094","DOIUrl":"https://doi.org/10.1111/pce.70094","url":null,"abstract":"<p><p>Early light-induced proteins (ELIPs) are pivotal for plant stress adaptation, yet their evolutionary and functional diversification across land plants remain unclear. Here, 454 ELIPs genes from 15 species (chlorophytes to angiosperms) were analysed using phylogenomics, cis-regulatory element mapping, transcriptomics, and transgenic validation. Phylogenetics classified ELIPs into four groups: Group 1 exclusive to non-seed plants (e.g., Physcomitrium patens), while angiosperms retained only Groups II-IV, reflecting lineage-specific evolutionary trajectories. Gene family expansion in angiosperms primarily occurred via whole-genome duplication, while bryophytes expanded through dispersed/tandem duplication, indicating distinct ecological adaptation strategies. Promoter analysis revealed bryophyte ELIPs uniquely enriched with ABA-responsive (ABRE) and drought-inducible (MBS) motifs, suggesting cis-regulatory innovation for water stress. Dehydration-rehydration transcriptomics revealed transient upregulation of eight P. patens ELIPs during dehydration, contrasting with the sustained AtELIP2 induction in Arabidopsis thaliana. Transgenic Arabidopsis overexpressing PpELIP1/9 exhibited enhanced drought tolerance, delayed chlorophyll degradation, increased lateral root proliferation under ABA treatment, and reduced oxidative damages via chloroplast-localised thylakoid stabilisation. Our results highlight the conserved role of ELIPs in photoprotection and their functional diversification in ABA-mediated drought adaptation, positioning bryophytes as reservoirs of ancestral stress resilience, bridging 450 million years of ELIP evolution and proposing a molecular framework for engineering stress-resilient crops through ELIP manipulation.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.3,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758817","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}
{"title":"Soybean Inositol Polyphosphate 5-Phosphatase 8 Confers Salt Tolerance by Reducing Sodium Influx Through Inositol 1,4,5-Trisphosphate Signalling.","authors":"Qi Jia, Yuan Chen, Defeng Kong, Hanyu Fan, Song Sun, Yuhang Liu, Jiahui Fu, Man-Wah Li, Fuk-Ling Wong, Qinghua Li, Kangjing Liang, Hon-Ming Lam, Wen-Xiong Lin","doi":"10.1111/pce.70071","DOIUrl":"https://doi.org/10.1111/pce.70071","url":null,"abstract":"<p><p>Evidence suggests that the metabolism of inositol and its derivatives may be involved in various biological processes including salt tolerance, but there has been limited understanding. Ectopic expression of Gs5PTase8, an inositol polyphosphate 5-phosphatase cloned from wild soybean (Glycine soja), significantly enhanced salt tolerance in cultivated soybean (Glycine max). In this follow up study, the overexpression of Gs5PTase8 was shown to improve salt tolerance in transgenic Arabidopsis thaliana, soybean hairy roots and composite plants, by preventing sodium (Na<sup>+</sup>) accumulation and maintaining lower sodium/potassium (Na<sup>+</sup>/K<sup>+</sup>) ratios in plants under salt stress. Additionally, the interactions between Gs5PTase8 and its substrate, inositol 1,4,5-trisphosphate (IP<sub>3</sub>), were investigated for their role in enhancing salt tolerance. Overexpressing Gs5PTase8 reduced IP<sub>3</sub> contents, probably due to its 5-phosphatase activity. Moreover, external supplementation of IP<sub>3</sub> could restore the Na<sup>+</sup> accumulation in the Gs5PTase8-overexpressing tobacco BY-2 cells experiencing salt stress. The proteomic data obtained by data-independent acquisition implied that the degradation of IP<sub>3</sub> or phosphatidylinositol 4,5-bisphosphate (PI(4,5)P<sub>2</sub>) by Gs5PTase8 may maintain the ion homoeostasis of plants under salt stress by influencing the cytosolic calcium (Ca<sup>2+</sup>) signalling and the salt overly sensitive pathways.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740762","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}
{"title":"Time-course transcriptome and proteomic dynamics during the de novo shoot organogenesis in Chinese fir (Cunninghamia lanceolata)","authors":"Wensha Ding, Shanwen Ye, Duoke Wu, Wanping Wang, Junjie Xu, Wenjia Wang, Changyang Cai, Chentao Lin, Xiangqing Ma, Qiang Zhu","doi":"10.1111/tpj.70360","DOIUrl":"https://doi.org/10.1111/tpj.70360","url":null,"abstract":"<div>\u0000 \u0000 <p><i>De novo</i> shoot organogenesis (DNSO) enables plants to regenerate shoots from various explants, offering valuable opportunities for research and plant biotechnology applications. While significant progress has been made in understanding regeneration in angiosperms, the regulatory mechanisms in gymnosperms, particularly Chinese fir (<i>Cunninghamia lanceolata</i>), remain poorly understood, despite its importance as a key timber species in China. This study successfully established an efficient DNSO protocol for Chinese fir, identifying six distinct stages in the process through cellular-level analysis. Time-course transcriptome and proteomics analyses revealed dynamic changes in mRNA and protein levels during regeneration. Notably, proteins showed more significant alterations across a broad range of biological processes, often independent of corresponding mRNA changes. Key pathways associated with ethylene metabolism and abiotic stress responses were enriched, highlighting their critical roles in regeneration. Further experiments confirmed that moderate osmotic stress treatments (150 m<span>m</span> mannitol) and ethylene treatment (100 μ<span>m</span> ACC and 5 μ<span>m</span> AgNO<sub>3</sub>) substantially enhanced DNSO efficiency. In summary, this study uncovers the molecular mechanisms underlying Chinese fir DNSO, providing valuable insights into improving plant regeneration efficiency in this economically important species. These findings contribute to advancements in plant biotechnology and sustainable forestry practices.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740173","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}
{"title":"Gene editing of clock components in Solanum lycopersicum: Effects on gene expression, development, and productivity","authors":"Benjamin Alary, Mostafa Mortada, Paloma Mas","doi":"10.1111/tpj.70383","DOIUrl":"https://doi.org/10.1111/tpj.70383","url":null,"abstract":"<div>\u0000 \u0000 <p>The circadian clock plays a crucial role in regulating key biological processes, including growth and development. While studies in the model plant <i>Arabidopsis thaliana</i> have significantly advanced our understanding of circadian function, recent research has also focused on crop species for improved yield and quality. In this study, we examined the rhythmic behavior and regulatory function of circadian clock components in tomato (<i>Solanum lycopersicum</i>). Time course analyses of gene expression over the circadian cycle revealed robust rhythmic oscillations in tomato leaves under free-running conditions. Comparative analyses showed similar peak phases for several clock genes in <i>Arabidopsis</i> and tomato, suggesting functional conservation. Rhythms in tomato fruits, however, showed reduced amplitude, slight phase changes, or arrhythmia, indicating organ-specific circadian variations. By using <i>CRISPR-Cas9</i> gene editing strategies (<i>clock</i><sup><i>crispr</i></sup>), we also showed that proper clock gene expression is essential for setting the phase in tomato plants. Leaf movement analyses also showed a phase change in the <i>clock</i><sup><i>crispr</i></sup> lines, correlating with shorter or longer periods. The <i>clock</i><sup><i>crispr</i></sup> lines also displayed distinct growth and developmental phenotypes that differ from those reported in the <i>Arabidopsis</i> clock mutant counterparts. Our transcriptomic analyses identified species-specific regulation of key target genes. The results offer mechanistic insights into the conserved and divergent molecular pathways governing circadian phenotypic variations between <i>Arabidopsis</i> and tomato plants.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717043","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}
{"title":"Salt-responsive SSN1 condensation in nucleus facilitates PIF4 degradation to regulate Arabidopsis salt tolerance","authors":"Qi Wang, Linwei Zhao, Tiantian Shao, Zilong Xu, Ziqiang Zhu","doi":"10.1111/tpj.70389","DOIUrl":"https://doi.org/10.1111/tpj.70389","url":null,"abstract":"<div>\u0000 \u0000 <p>Soil salinity is detrimental to crop yield and global food security. The most well-known adaptation strategy for plant salt tolerance is to activate the plasma membrane localized salt sensing and signaling pathway to extrude Na<sup>+</sup> from cytosol to apoplast. Here, we identify <i>Arabidopsis</i> transcriptional repressor protein SALT SIGNALING IN NUCLEUS 1 (SSN1) forms salt bodies in the nucleus through liquid–liquid phase separation upon salt stress. As a negative regulator in salt tolerance, the rapid salt-induced SSN1 condensation in the nucleus is required for SSN1 degradation. SSN1 also co-condenses with another negative regulator PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) through assembling the SALT OVERLY SENSITIVE 2 (SOS2)-PIF4 complex in the same salt body. We propose that in addition to the cell surface salt extrusion pathway, the formation of the salt body by SSN1 in the nucleus is essential for plant survival under salt stress.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717051","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}
{"title":"Comprehensive identification and analysis of clusters of tandemly duplicated genes reveal their contributions to adaptive evolution of green plants","authors":"Yuhang Yang, Qionghou Li, Hongxiang Li, Kaijie Qi, Zhihua Xie, Zewen Wang, Ying Zou, Baisha Huang, Jian Hu, Xin Qiao, Shaoling Zhang","doi":"10.1111/tpj.70370","DOIUrl":"https://doi.org/10.1111/tpj.70370","url":null,"abstract":"<div>\u0000 \u0000 <p>Tandem gene duplication occurred more frequently compared with the episodic whole-genome duplication (WGD), providing a continuous supply of genetic material for evolutionary innovation and adaptation to changing environments. The rising roles of clusters of tandemly duplicated genes (CTDGs) in the evolution of phenotypic diversity have been unraveled in mammals. However, the content and biological roles of CTDGs remain largely unknown in plants. Here, we comprehensively identified CTDGs in 220 published plant genomes representing major lineages of green plants. The number of CTDGs showed great variation across taxa, ranging from 0 to 6028. The size of CTDGs varied from 2 to 47 genes, with small clusters containing two members predominating. Interestingly, significant expansion of CTDGs was found in early-diverging land plants and is closely associated with the evolution of key traits (e.g., ABA response, plant cuticle, UV-B resistance) required for plants to conquer terrestrial environments. Functional enrichment analysis revealed conserved and specialized functional profiles among different sizes of CTDGs in both <i>Arabidopsis thaliana</i> and the bryophyte <i>Physcomitrium patens</i>. Small CTDGs were enriched in fundamental stress responses, including protein modification, signal transduction, and responses to diverse stress stimuli, while large CTDGs were enriched in more sophisticated processes such as plant hormone biosynthesis and signaling, plant–microbe interactions, and reproductive processes. Expression pattern analyses of CTDGs under different stress conditions in <i>A. thaliana</i> and <i>P. patens</i> revealed that the highest number of CTDGs showed differential expression under drought stress, suggesting important roles of CTDGs in the evolution of desiccation tolerance in early land plants. The results of this study provide new additions to our knowledge about the abundance of CTDGs across green plants and reveal their important contributions to enable plants to overcome stressful environments on land.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144716947","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}
{"title":"Breaking the silence: tethering a translational enhancer to improve transgene expression","authors":"Martin Balcerowicz","doi":"10.1111/tpj.70375","DOIUrl":"https://doi.org/10.1111/tpj.70375","url":null,"abstract":"<p>Genetic transformation has become a routine technique in plant biology: transgenes are widely used as tools in fundamental research, as expression systems for high-value proteins and—despite advances in CRISPR-based gene editing—remain the method of choice to introduce traits absent from a species' breeding pool. However, these applications are frequently hampered by gene silencing, which can lead to the decline or even complete loss of transgene expression over successive generations. This effect has been attributed to two major processes: transcriptional gene silencing (TGS) via methylation of the transgene DNA, and post-transcriptional gene silencing (PTGS) mediated by the RNA interference (RNAi) pathway (Molnar et al., <span>2011</span>). PTGS involves the formation of short-interfering RNAs (siRNAs) of 21–25 nucleotides that are complementary to the transgene's mRNA. These siRNAs are loaded into RNA-induced silencing complexes, guiding them to their target mRNA for degradation or translational inhibition. PTGS typically precedes TGS, and continuous production of siRNAs can trigger activation of RNA-directed DNA methylation of a transgene's promoter regions (Matzke & Mosher, <span>2014</span>).</p><p>Keith Slotkin and his lab investigate gene silencing mechanisms in plants, and as part of this broader effort, also explore strategies to improve transgene expression. They recently leveraged the RNA-binding protein BRUNO-LIKE 1 (BRN1) to establish an <i>in vivo</i> protein–mRNA tethering system (Cuerda-Gil et al., <span>2022</span>). BRN1 binds a seven-nucleotide recognition sequence in the 3′ UTR of the <i>SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1</i> (<i>SOC1</i>) transcript and thereby interferes with its translation (Kim et al., <span>2013</span>). A truncated BRN1 RNA-binding domain (BD), while still able to bind the <i>SOC1</i> 3′ UTR, does not repress translation and can be fused to other proteins to influence the fate of the tethered mRNA. For example, fusion of a deadenylase protein to BD triggered <i>SOC1</i> transcript deadenylation and subsequent degradation, while fusion of the conserved 40S ribosomal subunit RIBOSOMAL PROTEIN S6 (RPS6) increased translation efficiency (Cuerda-Gil et al., <span>2022</span>).</p><p>Senior Research Scientist Yu-Hung Hung, first author of the highlighted paper, extended this approach to test whether the BD-RPS6 tethering system can be used to improve expression of transgenes. As a target Hung and colleagues chose Cas9, a widely used transgene that generates a quantifiable output. They generated Cas9 expression constructs with different BRN1 binding site configurations at the 3′ end: no (0xBS), one (1xBS) or four (4xBS) BRN1 binding sites, or the full <i>SOC1</i> 3′ UTR (Figure 1A). These constructs were expressed together with a guide RNA targeting the <i>ALCOHOL DEHYDROGENASE 1</i> (<i>ADH1</i>) gene and transformed into Arabidopsis plants with or without the BD-RPS6 tethering system.</p><p>To","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 2","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70375","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144725747","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}
{"title":"PsoRPM3 Recognises the Meloidogyne incognita Effector MiTSPc to Trigger Defence Response in Prunus sogdiana.","authors":"Wenjiang Pu, Xuefeng Chen, Zhikun Liu, Haifeng Zhu, Sifang Luo, Kun Xiao, Jianfang Hu, Pingyin Guan","doi":"10.1111/pce.70086","DOIUrl":"https://doi.org/10.1111/pce.70086","url":null,"abstract":"<p><p>Phytoparasitic nematodes are among the most economically destructive plant pathogens. Large numbers of effectors secreted by phytoparasitic nematodes are delivered into host cells to facilitate susceptible invasion and maintain long-lasting parasitism in the host plants. Plant nucleotide-bound leucine-rich repeat (LRR) receptors (NLRs) directly or indirectly recognise pathogen-derived effectors to initiate innate immunity. In this study, we have identified Meloidogyne incognita secreted effectors MiTSPc and MiACPS, which can interact with resistance protein PsoRPM3 in Prunus sogdiana (P. sogdiana). In the leaves of PsoRPM3 transgenic tobacco plants and disease-resistant P. sogdiana lines, when the MiTSPc and MiACPS were transit expressed, significant hypersensitive response and high ion leakage rate were detected. Moreover, when the MiTSPc was silenced in M. incognita, galls were observed in the roots of PsoRPM3 transgenic tobacco plants. Co-localisation experiments have shown that MiTSPc and PsoRPM3 were overlapped. Our data revealed that LxxLxLxxN/CxL motif of PsoRPM3 LRR domain can recognise MiTSPc<sup>23-54aa</sup>. Taken together, the disease resistant protein PsoRPM3 can directly recognise M. incognita effector MiTSPc to deploy defence responses in P. sogdiana.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.3,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740761","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}