{"title":"A robust technique for gas-exchange measurements using petiole-cut Arabidopsis leaves in a whole plant chamber.","authors":"Satoru Naganawa Kinoshita, Iris Finkemeier","doi":"10.1093/pcp/pcaf083","DOIUrl":"10.1093/pcp/pcaf083","url":null,"abstract":"","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1255-1258"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Stomatal CO2 sensing in plants: control of gas exchange and interactions with environmental stimuli.","authors":"Yohei Takahashi, Hyunhee Joo, Nattiwong Pankasem, Po-Kai Hsu, Julian I Schroeder","doi":"10.1093/pcp/pcaf074","DOIUrl":"10.1093/pcp/pcaf074","url":null,"abstract":"<p><p>Stomatal pores in land plants rapidly and reversibly open and close in response to diurnal changes in leaf carbon dioxide (CO2) concentration. Studies have suggested that CO2 is sensed by guard cells with relevant amplifying contributions from mesophyll tissue. CO2 concentration changes trigger rapid signal transduction events involving protein phosphorylation in guard cells. Moreover, molecular crosstalk and physiological interactions of the stomatal CO2 response with other environmental conditions and stimuli, including light, temperature, drought, and abscisic acid, are reviewed here. Genetic studies have revealed several key genes and provided important insights into the stomatal CO2 sensors and signal transduction mechanisms. The primary CO2/HCO3- sensor in Arabidopsis guard cells was recently identified. Quantitative trait locus (QTL) analyses have shown that early guard cell CO2 signal transduction components regulate water use efficiency (WUE). In this review, we describe the molecular details of stomatal CO2 sensing by CO2/HCO3--induced interaction of two protein kinases, the HIGH LEAF TEMPERATURE 1 Raf-like kinase and the MPK4/MPK12 mitogen-activated protein kinases. The evolutionary emergence of, physiological relevance of, and potential for improvement of WUE of plants via the stomatal CO2 response and open questions in this research field are discussed.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1259-1273"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144554312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Salicylic acid-mediated competitive regulation of xylem vessel formation and defense responses in Arabidopsis thaliana.","authors":"Ya Ma, Rune Kurokawa, Chaokun Huang, Ryosuke Sano, Taku Demura, Misato Ohtani","doi":"10.1093/pcp/pcaf086","DOIUrl":"10.1093/pcp/pcaf086","url":null,"abstract":"<p><p>In vascular plants, xylem vessels transport water and contribute to structural integrity. As part of vessel formation, xylem cells deposit secondary cell walls (SCWs), which are composed of cellulose, hemicellulose, and lignin polymers. Under environmental challenges such as pathogen attack, a growth-defense trade-off limits xylem vessel development. Understanding the mechanism regulating this trade-off has implications for understanding of plant strategy to utilize their carbon resources because SCWs contain large amounts of densely packed high-carbon compounds. Here, we investigated the effect of pathogen responses induced by the peptide defense elicitor flagellin22 (flg22) on VASCULAR-RELATED NAC-DOMAIN7 (VND7)-dependent xylem vessel formation in Arabidopsis (Arabidopsis thaliana). Treatment with flg22 decreased xylem transport and delayed ectopic xylem vessel differentiation, including SCW deposition, in plants with a dexamethasone-inducible VND7 system, suggesting that the plant prioritized defense responses over xylem formation. Consistent with this, transcriptome analysis revealed that flg22 treatment suppressed SCW-related genes and activated immune-related genes. Salicylic acid (SA) treatment had a similar inhibitory effect on VND7-dependent xylem vessel formation, and the sid2-2 and npr1-1 mutants, which are defective in SA biosynthesis and signaling, respectively, did not exhibit flg22-induced inhibition of xylem transport activity; these highlight the role of SA, which is biosynthesized from phenylalanine during immune responses, as a key mediator of the competition between xylem vessel formation and immune responses. These findings provide insights into how plants flexibly regulate xylem development under biotic stress to optimize their development.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1360-1374"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikola Kořínková, Alexie Techer, Maria Majeská Čudejková, Dieu Thu Nguyen, David Kopečný, Bruno Contreras-Moreira, Pavla Navrátilová, Pascal Gantet, Véronique Bergougnoux
{"title":"Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach.","authors":"Nikola Kořínková, Alexie Techer, Maria Majeská Čudejková, Dieu Thu Nguyen, David Kopečný, Bruno Contreras-Moreira, Pavla Navrátilová, Pascal Gantet, Véronique Bergougnoux","doi":"10.1093/pcp/pcaf077","DOIUrl":"10.1093/pcp/pcaf077","url":null,"abstract":"<p><p>Cereal plants possess a fibrous root system in which crown roots form the major component. Crown roots develop post-embryonically from the lower, mostly underground nodes of the stem base. A strict spatiotemporal regulation of gene expression governs this process. Much of the knowledge about signaling pathways controlling crown root initiation (CRI) and development comes from rice. However, distinct regulatory mechanisms may have evolved in other cereals to adapt to different habitats. In this study, using a Crown Root Inducible System (CRIS), we aimed to investigate the early molecular regulation of barley CRI. We revealed dynamic transcriptomic changes within the first 24 hours following auxin stimulation. Among the differentially expressed genes, we identified orthologs of important CRI regulators from other cereals, demonstrating that CRIS is suitable for uncovering genes involved in CRI. Further, ATAC-seq revealed that CRI relies on changes in chromatin accessibility near root development-related genes and within distal intergenic regions. Finally, we focused on two transcription factors, HvNAC013 and CBF12C, which likely play roles in both CRI and abiotic stresses. By performing DAP-seq, we determined their genome-wide binding sites and identified their potential downstream targets. Data suggest that CBF12C is a putative target of HvNAC013, along with other auxin-responsive genes implicated in CRI. We propose that HvNAC013 and CBF12C function as part of a transcription factor network involved in CRI and potentially modulate root architecture in response to environmental conditions. This study enhances our understanding of the CRI mechanism in barley.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1284-1303"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Partial photoswitching of rod-shaped phycobilisome production in the cyanobacterium Synechocystis sp. PCC 6803.","authors":"Mutsumi Kubushiro, Takuto Otsu, Naomi Misawa, Masako Hamada, Toshihiko Eki, Shigeru Kawai, Yuu Hirose","doi":"10.1093/pcp/pcaf064","DOIUrl":"10.1093/pcp/pcaf064","url":null,"abstract":"<p><p>Certain cyanobacteria can alter the structure of their photosynthetic supercomplex phycobilisome (PBS) in response to changes in ambient light color. This process is known as chromatic acclimation (CA) and is classified into seven types (CA1-CA7), each involving distinct modifications of PBS structure. Among them, CA1 is defined as the regulation of the rod-shaped PBS in response to green and red light, maintaining the excitation balance between the two photosystems. Synechocystis sp. PCC 6803 (PCC 6803) is a widely used model cyanobacterium for photosynthesis research and harbors the CcaSR photosensory gene cluster for CA1. In this study, we investigated the wavelength dependence of the rod-shaped PBS production in PCC 6803. RNA-Seq analysis revealed that the expression of cpcL, which encodes a rod-membrane linker protein of rod-shaped PBS, is upregulated under a wide range of visible light (470-630 nm) and partially suppressed under violet (380-420 nm) and red to far-red light (680-720 nm) conditions. Low-temperature fluorescence emission spectra revealed that the ratio of rod-shaped PBS to hemi-discoidal PBS was highest under green light (530 nm), followed by red (660 nm) and far-red (700 nm) conditions. Furthermore, the isolation of intact PBS fractions using an improved procedure revealed the presence of rod-shaped PBS containing CpcL under these light conditions. The incomplete photoswitching of the rod-shaped PBS production may be due to the adaptation of the photosensory CcaSR system in PCC 6803, which lacks green-absorbing components in its PBSs and provides green-light rich environments in their cell aggregates.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1274-1283"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Gene expression and regulatory networks provide new insights into the similarity between nitrogen fixing and arbuscular mycorrhizal symbioses.","authors":"Zefeng Wu, Yali Sun, Jun Yang, Zigang Liu, Yining Niu, Xiaowei Zhang","doi":"10.1093/pcp/pcaf082","DOIUrl":"10.1093/pcp/pcaf082","url":null,"abstract":"<p><p>Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbuscular mycorrhizal symbiosis (AMS). A growing number of symbiosis-regulated genes have been characterized through either genetic analysis or phylogenomic profiling. However, the underlying similarities and specificities of the transcription regulatory machinery in AMS and NFS remain largely unclarified. Here, we systematically profiled the gene expression changes in three legume species, namely Medicago truncatula, Glycine max, and Lotus japonicus, during AMS and NFS. Additionally, we investigated gene expression changes in three non-legume plants, Solanum lycopersicum, Zea mays, and Oryza sativa, during AMS. We identified thousands of genes that were activated by AMS or NFS in their respective host plants. Through comparative genomics analysis, we systematically explored the conservation and specificity of genes responsive to AMS or NFS. Employing M. truncatula and G. max as illustrative cases, we harnessed the XGboost machine-learning model to construct co-expression-based gene regulatory networks (GRNs) for AMS and NFS within these two species. Through this approach, we successfully illuminated the similarities and unique features of the two symbiotic types at the GRN level. Further, utilizing known symbiosis genes as queries, we pinpointed a multitude of genes that are intimately associated with AMS and NFS. Overall, via in-depth gene expression profiling and regulatory network analysis, our results indicate that, while NFS in legumes has regulatory circuits similar to those of AMS, there exist certain symbiosis type-specific molecular components.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1330-1345"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Defective pollen meiosis in Arabidopsis due to combined arabinan and galactan insufficiency.","authors":"Takuma Kikuchi, Kouichi Soga, Toshihisa Kotake, Daisuke Takahashi","doi":"10.1093/pcp/pcaf085","DOIUrl":"10.1093/pcp/pcaf085","url":null,"abstract":"<p><p>The development of pollen is critical for seed plants and depends on precise cellular and molecular mechanisms. It is known that the cell wall plays a key role in the progression of pollen maturation. An earlier phase in pollen development is the meiosis of pollen mother cells (PMCs), a fundamental process for producing viable pollen grains. However, the significance of the cell wall during pre-meiosis processes has remained unclear. Pectin, a major component of the cell wall, accumulates abundantly in pollen. To investigate the significance of the cell wall during pre-meiosis and meiosis, we generated an arad1 gals2 gals3 triple mutant of Arabidopsis thaliana, lacking the genes responsible for normal synthesis of arabinan and galactan, which constitute the side chains of pectin. Although vegetative growth and cell wall properties were comparable in wild-type (WT) and arad1 gals2 gals3, the pollen development in the mutant failed during meiosis. Immunohistochemical analysis showed that pectic arabinan and galactan accumulated in WT PMCs before meiosis, but this was not observed in mutant PMCs. On the other hand, it was found that pistil development of WT and arad1 gals2 gals3 was comparable. These findings suggest that the transient accumulation of arabinan and galactan in PMCs before meiosis is crucial for pollen meiosis. We believe that this study is the first to demonstrate the critical role of cell wall components, specifically pectic arabinan and galactan, in the pre-meiosis processes of pollen development.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1346-1359"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Thai Q Dao, Colleen Drapek, Alexander Jones, Samuel Leiboff
{"title":"Comparing hormone dynamics in cereal crops via transient expression of hormone sensors.","authors":"Thai Q Dao, Colleen Drapek, Alexander Jones, Samuel Leiboff","doi":"10.1093/pcp/pcaf080","DOIUrl":"10.1093/pcp/pcaf080","url":null,"abstract":"<p><p>Although hormone biology is critical for plant breeding, complex phenotypic outputs make it difficult to compare across species. We used transient expression of hormone biosensors and transcriptomics to simplify this output and quantify gibberellic acid (GA) and auxin responses across multiple cereal crop genotypes and tissues. We show the GPS2 biosensor detects exogenous GA in maize, barley, sorghum, and wheat. Measuring across GA dosages, we detect tissue- and genotype-specific differences in GA sensor response with an unexpected drop in GPS2 output in the maize d1 GA biosynthesis mutant after GA treatment, likely reflecting differences in GA response across samples. We used RNA sequencing followed by ortholog prediction and Gene Ontology-term enrichment analysis to measure GA responses in leaves and floral tissues from maize wildtype, d1, and barley Golden Promise. We determine that cross-tissue, cross-genotype, and cross-species GA responses include downregulation of GA-INSENSITIVE DWARF1 and upregulation of α-Expansin1, independent of GA biosynthesis. We identify F-Box proteins, hexokinase, and AMPK/SNF1 protein kinase orthologs as unexpected cross-species GA-responsive genes. We then compared transient expression of DR5, DR5v2, and DII-mDII auxin reporters in barley and maize and find DR5v2 and DII-mDII are functional auxin reporters in both species.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1304-1320"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144650244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Arabidopsis SnRK2.9 interacts with FAH1 to regulate sucrose-induced anthocyanin.","authors":"Tiantian Dong, Yu Sun, Kaijing Zuo, Qijun Ma","doi":"10.1093/pcp/pcaf081","DOIUrl":"10.1093/pcp/pcaf081","url":null,"abstract":"<p><p>Sucrose has been found to possess regulatory characteristics in the biosynthesis of anthocyanin. The interplay between SnRK2s and the regulation of both anthocyanin production and sugar accumulation is significantly influential. However, a comprehensive understanding of the precise mechanism linking SnRK2s to anthocyanin remains limited. In the study, we have made a significant discovery regarding the role of the gene FAH1 (ferulate 5-hydroxylase)-mediated regulation of sucrose-induced anthocyanin biosynthesis in Arabidopsis. By employing a screening process using an Arabidopsis cDNA library with FAH1 as bait, it successfully identified protein kinase SnRK2.9, which is involved in the regulatory pathway. Subsequent pull-down and Co-IP assays provided further confirmation of the physical interaction between SnRK2.9 and FAH1. Moreover, our findings suggest that under high levels of sucrose exposure, SnRK2.9 negatively modulates both the stability and enzymatic activity of FAH1 protein. The research provides valuable insights into the regulatory mechanisms employed by plants to modulate the anthocyanin response triggered by sucrose.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1321-1329"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Integration of signals inducing reproductive phase transition occurs at the nodal enlarged vascular bundles in sacred lotus, Nelumbo nucifera.","authors":"Ryusei Waizumi, Sakura Ichinose, Misaki Inoue, Motoyuki Ishimori, Michio Shibata, Yohei Higuchi","doi":"10.1093/pcp/pcaf088","DOIUrl":"10.1093/pcp/pcaf088","url":null,"abstract":"<p><p>Sacred lotus (Nelumbo nucifera) is a perennial aquatic plant classified into basal eudicots, propagating through both sexual (flowering) and vegetative (clonal) reproduction. In lotus, the transition from sexual to clonal reproductive phases (swelled rhizome formation) is induced by short-day (SD) photoperiods, but the molecular mechanism remains unclear. Recent studies have shown that signals inducing reproductive phase transitions, such as flowering and storage organ formation, are integrated into the regulation of FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) family gene expression. Elucidating the expression dynamics of lotus FT/TFL1 genes is expected to deepen our understanding of the molecular mechanisms underlying different reproductive modes. In this study, we identified candidate FT/TFL1 genes involved in growth phase transition in lotus through spatiotemporal expression analyses and transgenic assays using Arabidopsis. Interestingly, clear correlations between the phase transition and expression changes of putative inducers of flowering and rhizome swelling, NnFT2 and NnFT3, were observed not in leaves, but in underground tissues, including nodes and internodes of the rhizome. NnBFT1, a putative floral inhibitor in lotus, may mediate the transition from sexual to clonal reproduction by suppressing floral development through SD-responsive upregulation. Furthermore, histological observations revealed that lotus possesses enlarged vascular bundles within its nodes, similar to those reported only in some species of monocots. Our results suggest that this distinctive tissue is where the crucial regulation of FT/TFL1 gene expression occurs. This study sheds light on the unique mechanism of reproductive phase transition in lotus and the novel function of nodes in plant propagation.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1375-1388"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144761078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}