生命科学最新文献

{"title":"AI-Driven Discovery of Dual-Function Peptides Stabilizes MYC2 to Combat Citrus Huanglongbing.","authors":"Xinxin Wang, Jianping Chen, Zongtao Sun, Hehong Zhang","doi":"10.1111/pce.70096","DOIUrl":"https://doi.org/10.1111/pce.70096","url":null,"abstract":"","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":"144751868","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,&nbsp;Mostafa Mortada,&nbsp;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>^{<i>crispr</i>}), 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>^{<i>crispr</i>} lines, correlating with shorter or longer periods. The <i>clock</i>^{<i>crispr</i>} 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,&nbsp;Linwei Zhao,&nbsp;Tiantian Shao,&nbsp;Zilong Xu,&nbsp;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⁺ 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,&nbsp;Qionghou Li,&nbsp;Hongxiang Li,&nbsp;Kaijie Qi,&nbsp;Zhihua Xie,&nbsp;Zewen Wang,&nbsp;Ying Zou,&nbsp;Baisha Huang,&nbsp;Jian Hu,&nbsp;Xin Qiao,&nbsp;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":"&lt;p&gt;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., &lt;span&gt;2011&lt;/span&gt;). 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 &amp; Mosher, &lt;span&gt;2014&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;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 &lt;i&gt;in vivo&lt;/i&gt; protein–mRNA tethering system (Cuerda-Gil et al., &lt;span&gt;2022&lt;/span&gt;). BRN1 binds a seven-nucleotide recognition sequence in the 3′ UTR of the &lt;i&gt;SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1&lt;/i&gt; (&lt;i&gt;SOC1&lt;/i&gt;) transcript and thereby interferes with its translation (Kim et al., &lt;span&gt;2013&lt;/span&gt;). A truncated BRN1 RNA-binding domain (BD), while still able to bind the &lt;i&gt;SOC1&lt;/i&gt; 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 &lt;i&gt;SOC1&lt;/i&gt; transcript deadenylation and subsequent degradation, while fusion of the conserved 40S ribosomal subunit RIBOSOMAL PROTEIN S6 (RPS6) increased translation efficiency (Cuerda-Gil et al., &lt;span&gt;2022&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;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 &lt;i&gt;SOC1&lt;/i&gt; 3′ UTR (Figure 1A). These constructs were expressed together with a guide RNA targeting the &lt;i&gt;ALCOHOL DEHYDROGENASE 1&lt;/i&gt; (&lt;i&gt;ADH1&lt;/i&gt;) gene and transformed into Arabidopsis plants with or without the BD-RPS6 tethering system.&lt;/p&gt;&lt;p&gt;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":"GCN1 Regulates Translation of Chloroplast-Encoded Genes in Response to Light via the Nuclear Gene-Encoded Protein RH39.","authors":"Xiaona Cui, Meijun Chen, Shuhao Zhou, Mengyang Lv, Linjuan Wang, Kaili Gao, Jian-Kang Zhu, Hairong Zhang","doi":"10.1111/pce.70087","DOIUrl":"https://doi.org/10.1111/pce.70087","url":null,"abstract":"","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":"144740760","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":"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^23-54aa. 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}

{"title":"Nitric oxide delays floral transition in Arabidopsis by inhibiting histone deacetylases HDA5 and HDA6","authors":"Wenwen Zhu,&nbsp;Lei Wang,&nbsp;Jinzheng Wang,&nbsp;Ni Zhan,&nbsp;Zhongtian Shi,&nbsp;Yuying Sun,&nbsp;Qiang Lv,&nbsp;Yong Hu,&nbsp;Fang Bao,&nbsp;Ling Li,&nbsp;Yikun He,&nbsp;Yu Wang","doi":"10.1111/tpj.70379","DOIUrl":"https://doi.org/10.1111/tpj.70379","url":null,"abstract":"<div>\u0000 \u0000 <p>Nitric oxide (NO), a reactive small molecule, plays a critical role in various developmental and physiological processes in living organisms. Previous studies by our group revealed that NO delays flowering in Arabidopsis by increasing transcript levels of the flowering repressor <i>FLOWERING LOCUS C</i> (<i>FLC</i>). In this study, we further investigated the molecular mechanism by which NO regulates <i>FLC</i> expression. Genetic experiments demonstrated that NO-induced delayed flowering specifically depends on elevated <i>FLC</i> transcript levels. Chromatin Immunoprecipitation assays revealed that NO significantly enhances histone H3 acetylation at the <i>FLC</i> locus. Biochemical analyses further showed that NO reduces total histone deacetylase activity through <i>S</i>-nitrosylation of histone deacetylases HDA5 and HDA6. Additionally, we identified and evaluated potential <i>S-</i>nitrosylation sites on HDA5 and HDA6, revealing their effects on deacetylase activity and floral regulation. Collectively, our findings uncover a novel mechanism by which NO mediates epigenetic modification to modulate flowering in Arabidopsis. This study sheds light on the functional network linking NO signaling, epigenetic modification, and flowering.</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":"144717041","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":"Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses","authors":"Sean M. Robertson,&nbsp;Solihu Kayode Sakariyahu,&nbsp;Elisa Gan,&nbsp;Obaid Maqsood,&nbsp;Asher Pasha,&nbsp;Nicholas J. Provart,&nbsp;Olivia Wilkins","doi":"10.1111/tpj.70349","DOIUrl":"https://doi.org/10.1111/tpj.70349","url":null,"abstract":"<p>Growth-limiting droughts (GLD) impair tissue expansion and delay developmental transitions but are often not considered as stressors, as many physiological traits are only slightly altered relative to well-watered counterparts. Concurrently, cell size, biochemical makeup, and transcriptome profiles vary along the leaf blade in accordance with the partitioning of distinct functions to spatially defined regions of the leaf. This suggests that because different parts of the leaf have underlying differences in their transcriptome profiles, they might respond to GLD in distinctive ways. Moreover, how antagonistic stressors influence physiology and gene expression in different zones of leaves is an open question. In this study, we profiled growth, anatomy, and gas exchange in Asian rice (<i>Oryza sativa</i>) leaves developed in well-watered and GLD conditions, with or without a secondary heat shock. We dissected leaves into seven equal-length segments for transcriptome analysis in these conditions. We hypothesized that GLD would make the leaves more sensitive to heat shock and would disrupt the underlying heterogeneity of the leaf transcriptome. GLD plants were more strongly affected by heat shock with respect to gas exchange and the number and types of genes that were differentially expressed and that these differences varied along the leaf blade. We developed an eFP browser tool with these data to facilitate exploration and hypothesis testing. These findings show that even mild drought treatments are sufficient to impact responses to antagonistic stressors and that substantial within-organ variance exists with respect to stress responses.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70349","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144716697","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":"TaSG-D1–TaGAMyb signaling module regulates seed weight in wheat (Triticum aestivum L.)","authors":"Yan Zhou,&nbsp;Guangxian Cui,&nbsp;Shijun Wei,&nbsp;Xingyuan Xi,&nbsp;Jiaqi Zhang,&nbsp;Hongjiao Jiang,&nbsp;Jie Cao,&nbsp;Baoyue Zhang,&nbsp;Yumei Zhang,&nbsp;Huiru Peng,&nbsp;Yingyin Yao,&nbsp;Zhaorong Hu,&nbsp;Zhongfu Ni,&nbsp;Ive De Smet,&nbsp;Qixin Sun,&nbsp;Mingming Xin","doi":"10.1111/tpj.70377","DOIUrl":"https://doi.org/10.1111/tpj.70377","url":null,"abstract":"<p>Grain weight is one of the critical determinants of wheat (<i>Triticum aestivum</i> L.) yield, and understanding its genetic and molecular mechanisms is essential for improving crop productivity. Here, we find that <i>TaSG-D1</i>, which encodes an STKc-GSK3 kinase, negatively regulates grain weight. TaSG-D1 interacts with and phosphorylates TaGAMyb to reduce its degradation. Overexpression of <i>TaGAMyb</i> results in decreased grain length and weight, whereas its knockout increases both agronomic traits in wheat. Further investigation reveals that TaGAMyb directly activates the expression of <i>TaCKX2.2.1</i>, a negative regulator of grain development. Transcriptome profiling shows differential expression of <i>TaCKX2.2.1</i> in 15-DAP grain of WT and <i>TaGAMyb</i> knockout lines, ultimately leading to a decreased concentration of active cytokinin in grains. Taken together, our findings demonstrate that <i>TaSG-D1</i> negatively regulates grain development by increasing the protein abundance of transcription factor TaGAMyb, which in turn promotes the expression of downstream gene <i>TaCKX2.2.1</i>, a key regulator of cytokinin signaling.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70377","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144716695","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}