Tomoaki Muranaka, Genki Yumoto, Mie N Honjo, Atsushi J Nagano, Ji Zhou, Hiroshi Kudoh
{"title":"Coincidence of the Threshold Temperature of Seasonal Switching for Diel Transcriptomic Oscillations and Growth.","authors":"Tomoaki Muranaka, Genki Yumoto, Mie N Honjo, Atsushi J Nagano, Ji Zhou, Hiroshi Kudoh","doi":"10.1093/pcp/pcaf092","DOIUrl":"https://doi.org/10.1093/pcp/pcaf092","url":null,"abstract":"<p><p>Predicting plant responses to global warming is essential for ecosystem management and crop yields. As many genes are controlled by the circadian clock, understanding the effects of temperature on transcriptomic rhythmicity under natural conditions is necessary. Here, we detected diel rhythmic genes (DRGs) in Arabidopsis halleri in four seasons. In winter, the expression of most DRGs showed low amplitude but kept at high levels, consistent with the high enrichment of cold response genes. We defined 204 core DRGs that were rhythmic over at least three seasons. Using machine-learning, sampling time was successfully decoded by these 204 core DRGs across a year. In the three-dimensional principal component space for core DRGs, the diel transcriptomes appeared as four circular orbits with different diameters arranged in seasonal order, shaping cone like structure. Each transcriptome was mapped to the surface of the cone. The geometrical distance from the cone axis to the single-time-point transcriptome was defined as the amplitude of the transcriptomic clock. The amplitude showed seasonal switching with a sudden rhythm attenuation at 7 °C and lower. Additionally, field monitoring of the plant size revealed growth arrest at similar temperatures. These results imply cooperation in the temperature-dependent regulations of circadian rhythmicity and growth, highlighting the importance of the circadian clock in predicting plant responses to climate change.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144837471","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":"The DCD domain-containing protein HaB2 enhances sunflower resistance to Orobanche cumana via the ABA signaling pathway.","authors":"Ruixuan Zhao, Lele Li, Rui Xu, Runyao Bai, Aodun Bao, Heer Qing, Fang Yan, Xiaofei Lin, Hada Wuriyanghan","doi":"10.1093/pcp/pcaf089","DOIUrl":"https://doi.org/10.1093/pcp/pcaf089","url":null,"abstract":"<p><p>Broomrape (Orobanche cumana) is a major threat to sunflower (Helianthus annuus) production. Although B2 proteins, a class of DCD (development and cell death) domain-containing proteins, are reported to play a role in responses to a variety of abiotic stresses in plants, their function in biotic stress remains unclear. This study explored the role of HaB2 in sunflower resistance to O. cumana, focusing on its regulation through the ABA signaling pathway. Our results show that O. cumana infection and exogenous ABA treatment strongly induce HaB2 expression in sunflower root. Silencing HaB2 increases parasite attachment, while over-expression of HaB2 reduces the formation of haustoria and xylem bridges. The DCD domain is essential and sufficient for HaB2 resistance function. In addition, we found a physiological interaction between HaB2 and the phosphatase HaFyPP3, whereas HaFyPP3 interacts with the ABA-responsive transcription factor HaABI5. Exogenous application of ABA exhibits a resistance phenotype consistent with that by HaB2 over-expression plant. HaABI5 promotes the expression of HaB2 by binding to the ABRE element on its promoter and therefore enhance sunflower resistance, while HaFyPP3 dampens negatively regulates HaB2-mediated resistance by possibly dephosphorylating both ABI5 and HaB2. These results suggest that HaB2 acts as a positive regulator to enhance sunflower resistance to broomrape through involvement in the ABA signaling pathway, providing new insights into ABA-mediated biotic stress resistance and potential targets for exploitation of superior O. cumana resistant sunflower varieties by molecular breeding.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144837474","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}
Anastasiia Kolomiiets, Oleksandr Bren, Pavel Přibyl, Jana Kvíderová, Lenka Procházková, Ekaterina Pushkareva, Josef Elster, Burkhard Becker
{"title":"Unveiling the molecular mechanisms of the stress resilience of High Arctic Klebsormidium flaccidum: A multifaceted study.","authors":"Anastasiia Kolomiiets, Oleksandr Bren, Pavel Přibyl, Jana Kvíderová, Lenka Procházková, Ekaterina Pushkareva, Josef Elster, Burkhard Becker","doi":"10.1093/pcp/pcaf091","DOIUrl":"https://doi.org/10.1093/pcp/pcaf091","url":null,"abstract":"<p><p>The green alga Klebsormidium is found worldwide in terrestrial and freshwater habitats. A novel strain was isolated from biological soil crusts on Breinosa Mountain in Svalbard (High Arctic, 78°N) to investigate its adaptation to extreme Arctic conditions, characterized by low temperatures and short periods of snow-free ground. Genetic analyses confirmed the strain's identity as Klebsormidium flaccidum, showing high genetic similarity to strains from polar and temperate habitats. This study explored the effects of nitrogen starvation, cold stress, desiccation, and freezing, focusing on molecular responses and stress resilience. Nitrogen starvation strongly impacted metabolic activity, while cold and desiccation stress had more subtle effects, with K. flaccidum showing permanent stress-related gene expression instead of acute responses. Cold acclimation was found to enhance desiccation and freezing tolerance, while nitrogen starvation worsened the effects of these stresses. These results suggest that K. flaccidum CCALA 1182 is inherently capable of withstanding fluctuating environmental stresses, highlighting its potential for survival in diverse and harsh ecosystems.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144837475","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}
Jing Zhang, Hendry Susila, Sadia Majeed, Gonzalo M Estavillio, Harsh Raman, Barry J Pogson, Robert T Furbank
{"title":"Pod Photosynthesis: A New Frontier for Developing Stress-Resilient and High-Yielding Crops.","authors":"Jing Zhang, Hendry Susila, Sadia Majeed, Gonzalo M Estavillio, Harsh Raman, Barry J Pogson, Robert T Furbank","doi":"10.1093/pcp/pcaf090","DOIUrl":"https://doi.org/10.1093/pcp/pcaf090","url":null,"abstract":"<p><p>Burgeoning global demand for crop products and the negative impact of climate change on crop production are driving the need to improve yield by developing new elite crop varieties without expanding planted area or increasing agronomic inputs. Improvement in photosynthesis is critical for enhancing crop productivity. Even though leaf photosynthesis is well-studied, the photosynthetic potential of non-foliar green tissues like pods in Brassicaceae and Fabaceae species remains underexplored. This review emphasizes pod photosynthesis in determining seed yield and quality in Brassicaceae and Fabaceae crops. At present, accurate and efficient phenotyping methods are unavailable, limiting understanding and genetic improvement of pod photosynthesis. Novel approaches like chlorophyll fluorescence and hyperspectral reflectance are promising for high-throughput phenotyping of pod photosynthetic traits. This review further discusses genetic targets and regulatory mechanisms for enhancing pod photosynthesis, including transcription factors like GLK and GATA that may regulate photosynthetic capacity in pods, suggesting potential genetic manipulation strategies to boost crop productivity. In conclusion, unlocking the genetic and physiological bases of pod photosynthesis offers opportunities for advancing crop breeding to ensure sustainable food security amidst climate change and increasing global population pressures. Future research should focus on developing high-throughput phenotyping tools and elucidating genetic pathways to maximize pod photosynthesis in crops.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874891","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}
Chiasa Uragami, Koki Mitani, Nao Yukihira, Alastair T Gardiner, Richard J Cogdell, Hideki Hashimoto
{"title":"Photophysical Consequences of Spheroidene Reconstitution in LH1 of Rsp. rubrum: Improved Energy Transfer and Altered Photoprotection.","authors":"Chiasa Uragami, Koki Mitani, Nao Yukihira, Alastair T Gardiner, Richard J Cogdell, Hideki Hashimoto","doi":"10.1093/pcp/pcaf087","DOIUrl":"https://doi.org/10.1093/pcp/pcaf087","url":null,"abstract":"<p><p>Carotenoids are multifunctional pigments that play indispensable roles in photosynthesis, serving both to harvest light and to safeguard the system against photo-induced damage. In purple photosynthetic bacteria, these pigments, alongside bacteriochlorophyll (BChl) a, initiate the primary photochemical process by capturing solar energy within light-harvesting (LH) complexes. The excitation energy absorbed by carotenoids is efficiently transferred to BChl a and subsequently to the reaction center, where charge separation drives energy conversion. Improving the efficiency of excitation energy transfer (EET) from carotenoids to BChl a is a promising strategy for advancing bio-inspired light-harvesting systems and artificial photosynthesis. Here, we reconstituted spheroidene, a carotenoid known to achieve ~90% EET efficiency in the LH2 complex of Rhodobacter sphaeroides strain 2.4.1, into the carotenoidless LH1 complex of Rhodospirillum (Rsp.) rubrum strain G9+. This modification was anticipated to enhance EET efficiency relative to the native LH1 complex of Rsp. rubrum strain S1. Fluorescence excitation spectroscopy confirmed an improvement in EET. Surprisingly, sub-nanosecond time-resolved absorption spectroscopy revealed the emergence of a long-lived BChl a cation, an unusual state not typically observed in native systems. This phenomenon coincided with shortened triplet lifetimes of both carotenoid and BChl a, implying altered photoprotective dynamics. These findings suggest that while spheroidene facilitates efficient energy transfer in LH1 from Rsp. rubrum, it may also perturb the native protein environment, potentially compromising photoprotection. Our study underscores the delicate balance between energy transfer and photostability, offering new insights into the design of robust and efficient artificial photosynthetic systems.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144744535","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":"Chlorophyll Reconstitution of Photosynthetic Light-Harvesting Complexes.","authors":"Yoshitaka Saga, Shota Kawato, Jiro Harada","doi":"10.1093/pcp/pcaf084","DOIUrl":"https://doi.org/10.1093/pcp/pcaf084","url":null,"abstract":"<p><p>Light-harvesting complexes (LHCs) play crucial roles in efficient photoenergy conversion and photoprotection of photosynthetic systems. In LHCs, functional pigments such as chlorophylls (Chls), bacteriochlorophylls (BChls), and carotenoids are sophisticatedly assembled with the help of polypeptides. The pigment assemblies in LHCs control the site-energy of each pigment, excitonic interactions among pigments, and excitation energy gradient in the protein matrix, as well as the formation and stability of the protein structure. In vitro reconstitution of LHCs is promising in understanding these structural and functional mechanisms of LHCs. In this review, we summarize two strategies of pigment reconstitution of LHCs; one is the formation of LHCs from a mixture of photosynthetic pigments and denatured polypeptides by their self-assembly, and the other is pigment substitution by the insertion of exogenous pigments into apoproteins partially lacking bound pigments. Next, we overview reconstitution studies of major LHC II derived from oxygenic photosynthetic organisms and core and peripheral antenna proteins of purple photosynthetic bacteria. Here, we focus on substituting Chls and BChls, key pigments in photosynthesis, in LHCs by the reconstitution. (B)Chl reconstitution of LHCs has allowed us to change essential parameters for the pigment-protein interactions and photofunctions, deepening our understanding of the molecular basis of the efficient light-harvesting functions. Reconstitution of LHCs will also be helpful for the modification and design of pigment-protein complexes toward utilization of sunlight energy for global problems on agricultural productivity and bioenergy production.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732888","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":"Correction to: A Comprehensive Study of Light Quality Acclimation in Synechocystis Sp. PCC 6803.","authors":"","doi":"10.1093/pcp/pcaf049","DOIUrl":"10.1093/pcp/pcaf049","url":null,"abstract":"","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"971"},"PeriodicalIF":4.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12290278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120523","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":"Global identification of AGO3-RNA interactions reveals targets of small RNA-mediated gene regulation in Chlamydomonas reinhardtii.","authors":"Suzuna Murakami, Hiroki Takahashi, Kaede Shimizu, Tomohito Yamasaki","doi":"10.1093/pcp/pcaf040","DOIUrl":"10.1093/pcp/pcaf040","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) form complexes with Argonaute (AGO) proteins and bind to mRNAs with complementary sequences to repress their expression. Organisms typically possess several hundred miRNAs that regulate diverse aspects of biology. Although the roles of miRNAs have been elucidated in multicellular organisms, they remain largely unexplored in unicellular organisms. Identifying miRNA target genes remains challenging in the green alga Chlamydomonas (Chlamydomonas reinhardtii), the first unicellular organism in which miRNAs were discovered. Previous computational and sequencing-based approaches, such as miRNA-mRNA complementarity predictions, RNA-seq, and Ribo-seq, have struggled to identify Chlamydomonas miRNA targets. While similar technical difficulties exist in animals, crosslinking immunoprecipitation followed by sequencing has overcome these challenges. This method involves ultraviolet-mediated crosslinking of RNA-binding proteins (RBPs) to their target RNAs in living cells, followed by partial RNase digestion, immunopurification, and sequencing to map RBP-associated RNAs across the genome. Here, we performed high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) to generate a global AGO3-RNA interaction map. We identified 120 mRNAs derived from nuclear genes and two mRNAs derived from chloroplast genes. Expression levels of the nuclear gene CAS and chloroplast gene petA were higher in an ago3 mutant than in wild-type Chlamydomonas, suggesting that AGO3 represses the expression of the genes identified through HITS-CLIP analysis. Our study demonstrates that HITS-CLIP analysis is now feasible for any RBP in Chlamydomonas, offering new opportunities to uncover the functions of RBPs of interest.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"940-955"},"PeriodicalIF":4.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12290286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021123","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":"Juvenile-to-adult phase transition in a common wheat cultivar Norin 61, and accompanying changes in leaf transcriptome.","authors":"Kanata Senoo, Shunsuke Yoshioka, Koichi Yamamori, Shuhei Nasuda, Takanori Yoshikawa","doi":"10.1093/pcp/pcaf034","DOIUrl":"10.1093/pcp/pcaf034","url":null,"abstract":"<p><p>Higher plants experience morphological and physiological changes during the vegetative stage called juvenile-to-adult (JA) phase transition. Despite the advanced studies in Arabidopsis, maize, and rice, the JA phase transition remains unexplored in wheat. This study aimed to elucidate when and how the transition occurs in wheat by investigating the temporal changes in leaf morphology, expression of its regulators, transcriptome, and photosynthetic activity in the common wheat cultivar Norin 61. As a result, leaf blade size, leaf tip shape, and trichome density on leaf blades exhibited major changes from the first to second leaf stages. The expression level of microRNA 156, a regulator of JA phase transition in plants, was the highest in the first leaf stage and decreased following the plant growth, whereas that of its targets, SQUAMOSA PROMOTER BINDING PROTEIN-like (SPL) genes, increased. Additionally, transcriptome profiles dramatically changed from the second to third leaf stages and from the fourth to fifth leaf stages, which could be characterized by the change in activity of photoreactions, material transport, and phytohormone signaling. Unlike rice, wheat showed high photosynthetic rates per unit area even in the first leaf, which may be a unique and noteworthy characteristic in wheat. Taken together, we conclude that wheat initiates the JA phase transition after the first leaf stage and reaches the adult phase before the fourth leaf stage; it subsequently enters the reproductive stage. The present study will provide a foundation for advanced studies on wheat JA phase transition.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"900-911"},"PeriodicalIF":3.9,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005271","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":"In-depth amino acid mutational analysis of the key interspecific incompatibility factor Stigmatic Privacy 1.","authors":"Yoshinobu Kato, Shun Tadokoro, Shota Ishida, Maki Niidome, Yuka Kimura, Seiji Takayama, Sota Fujii","doi":"10.1093/pcp/pcaf039","DOIUrl":"10.1093/pcp/pcaf039","url":null,"abstract":"<p><p>In plants, there is an active prezygotic interspecific-incompatibility mechanism to prevent unfavorable hybrids between two species. We previously reported that an uncharacterized protein with four-transmembrane domains, named as Stigmatic Privacy 1 (SPRI1), is responsible for rejecting heterospecific pollen grains in Arabidopsis thaliana. However, the lack of notable functional domains in SPRI1 has limited our understanding of its biochemical properties. In this study, we conducted a functional analysis of the SPRI1 protein through point-mutational experiments and biochemical analysis. We explored the molecular regulatory mechanisms of SPRI1 and the relationships with its function. Alanine- and glycine-scanning experiments together with the evolutional analysis showed that the structural integrity of the C-terminal regions of the extracellular domain of this protein is important for its function. In addition, we found two cysteines (C67 and C80) within the extracellular domain that may be involved in the formation of intermolecular disulfide bonds. These cysteine residues are required for the stabilization of the SPR1 protein. Furthermore, SPRI1 may form homo-multimers and is present as part of a ∼300 kDa complex. Our present study indicates that SPRI1 forms large protein machinery for the rejection of hetero-specific pollen in stigmatic papilla cells.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"926-939"},"PeriodicalIF":4.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12290284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094679","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}