Ang-Yu Liu, Prescott O Jeckel, Min May Wong, Diane C Bassham, Gustavo C MacIntosh
{"title":"Vacuolar phosphatases are essential for efficient nucleotide salvage in Arabidopsis.","authors":"Ang-Yu Liu, Prescott O Jeckel, Min May Wong, Diane C Bassham, Gustavo C MacIntosh","doi":"10.1093/jxb/eraf168","DOIUrl":"https://doi.org/10.1093/jxb/eraf168","url":null,"abstract":"<p><p>The salvage pathway that recycles nucleotides from RNA is an important contributor to cellular homeostasis. In Arabidopsis, RNA salvage occurs in the vacuole, in a process started by RNS2. Defects in this pathway lead to constitutive autophagy. How nucleosides are generated from RNS2-catalyzed RNA degradation remains unclear. Using a combination of biochemistry and molecular genetics, we showed that RNS2 produces 2',3'-cAMP and 3'-AMP from poly(A) degradation but only 2',3'-cUMP from poly(U). Mutants lacking PAP26, the major vacuolar acid phosphatase (APase), displayed increased basal autophagy that was rescued by inosine treatment, mirroring rns2 phenotypes. PAP26 deficient vacuoles have lower total APase activity than WT, but nucleotide processing is not fully disrupted. Further analyses showed that VSP3 also contributes to the total vacuolar APase activity. Nucleotide metabolism in pap26 vsp3 double mutants is severely disrupted, and mutant vacuoles accumulate 3'-NMP, 5'-NMP, and surprisingly 2'-AMP. We propose that PAP26 and VSP3 are the main APases involved in vacuolar RNA salvage. In addition, our results suggest that other activities, including cyclic phosphodiesterases and possibly a 5'-NMP-producing exoribonuclease, are needed to facilitate this process in Arabidopsis, producing the metabolites that are transported to the cytoplasm to maintain nucleotide homeostasis.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988299","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":"Panicle temperature explains contrasting yield responses of rice genotypes to elevated CO2 and increased temperature in T-FACE environments.","authors":"Haozheng Li, Liping Shao, Hongying Tang, Jiao Chen, Ting Yuan, Xiaomeng Chen, Huatang Meng, Dong Xiang, Rongxin Xu, Qingtian Liu, Kun Liu, Zijuan Liu, Xuanhe Guo, Gang Li, Weiping Chen, Weihong Luo, Xinyou Yin","doi":"10.1093/jxb/eraf170","DOIUrl":"https://doi.org/10.1093/jxb/eraf170","url":null,"abstract":"<p><p>Elevated CO2 increases, while high temperature decreases, rice yield. We hypothesize, the interplay between these opposite effects vary across genotypes and these variations are associated with abilities of genotypes in avoiding and tolerating stress. We evaluated Japonica genotype (Changyou5) and Indica genotype (Yangdao6) under combinations of two CO2-levels (ambient and enriched to 590 μmol mol-1) and two canopy temperatures (ambient and warmed by 2.0 ºC) in Temperature-by-Free-Air-CO2-Enrichment systems over two seasons. The elevated-CO2 fully offset the adverse effects of the elevated-temperature on grain yield of Yangdao6 but failed to do so for Changyou5. Yangdao6 increased yield by 20.0%, while Changyou5 decreased it by 7.8% under the combined elevated-CO2 and elevated-temperature. This genotypic difference was partly due to higher leaf-nitrogen content of cv. Yangdao6, resulting in superior light conversion efficiency. However, it was more explained by a comparatively smaller decrease in spikelet fertility (thus, harvest index) in Yangdao6, mainly resulting from lower panicle temperature during flowering. The lower panicle temperature in Yangdao6 was due to earlier flowering hours as well as to higher panicle-nitrogen content that presumably led to more transpirational cooling. The above key genotypic traits could be explored in rice breeding programs to improve yield resilience to climate change.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143994430","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":"Knockout of an SPX-related gene for polyphosphate synthetase accelerates phosphate-starvation responses in the oleaginous microalga Nannochloropsis oceanica.","authors":"Kumiko Okazaki, Koichi Hori, Masako Iwai, Tomokazu Kurita, Shinsuke Shimizu, Seiji Nomura, Fumihiko Saito, Shinichiro Maeda, Akihide Takami, Takashi Yamamoto, Hiroyuki Ohta, Atsushi Sakamoto","doi":"10.1093/jxb/eraf171","DOIUrl":"https://doi.org/10.1093/jxb/eraf171","url":null,"abstract":"<p><p>SPX domain-containing proteins are important for phosphate (Pi) signaling and homeostasis in various eukaryotes. Genomic and transcriptomic analyses of the oleaginous microalga Nannochloropsis oceanica identified four genes encoding SPX family members with distinct domain architectures: SPX (NoSPX1), SPX-VTC (NoSPX2), SPX-EXS (NoSPX3), and SPX-MFS (NoSPX4). These NoSPX genes responded differentially to Pi deprivation, with NoSPX1 and NoSPX2 expression being significantly upregulated. NoSPX1 encodes an essential nuclear protein of unknown function and NoSPX2 encodes a vacuolar or acidocalcisomal protein homologous to the vacuolar transporter chaperone 4 that catalyzes polyphosphate production for vacuolar phosphorus storage. Disruption of NoSPX2 diminished polyphosphate levels and slowed the net uptake of external Pi, confirming its role in polyphosphate biosynthesis and Pi homeostasis. Furthermore, Nospx2 mutant cells accumulated significantly more triacylglycerol and greater biomass and had enlarged lipid droplets under Pi deficiency compared to control cells. Together with these augmented Pi starvation responses, we observed a marked upregulation of genes involved in autophagy and lipid transfer across organellar membranes and the downregulation of photosynthesis-related genes, likely reallocating resources toward lipid biosynthesis. These results suggest that inadequate polyphosphate storage accelerates Pi starvation responses in microalgae, providing potential strategies for enhancing microalgal triacylglycerol accumulation and lipid productivity.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022007","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}
Sebastian Nw Hoernstein, Alessandra A Miniera, Ralf Reski
{"title":"Acylamino acid-releasing enzyme (AARE), a bifunctional protease with a potential role in aging.","authors":"Sebastian Nw Hoernstein, Alessandra A Miniera, Ralf Reski","doi":"10.1093/jxb/eraf169","DOIUrl":"https://doi.org/10.1093/jxb/eraf169","url":null,"abstract":"<p><p>Acylamino acid-releasing enzyme (AARE) is an evolutionary deeply conserved bifunctional serine protease. In its exopeptidase mode, AARE cleaves N-terminally acetylated or otherwise blocked amino acids from the N-terminus of peptides and probably even intact proteins. In its endopeptidase mode, AARE cleaves oxidised proteins at internal positions. Although AARE function was discovered 50 years ago and enzymes from various organisms have been characterized biochemically, the precise role of this protease in cellular physiology remains elusive. Several other names for AARE do exist in literature, such as acylpeptide hydrolase (APEH/ACPH), acylaminoacyl peptidase (AAP) and oxidised protein hydrolase (OPH). Recently, the first AARE null mutants have been described in the model moss Physcomitrella. Comparisons with T-DNA mutants in Arabidopsis revealed a role of AARE in the timing of the developmental transition from the vegetative to the reproductive state as well as in the determination of life span. Loss of AARE function was accompanied by a striking increase in oxidised proteins, which is a hallmark of aging. In mammals, AARE activity is linked to proteasomal function, and dysregulation of AARE function has been observed in different types of cancer and age-related pathologies. Here, we compile the current knowledge on molecular and biological functions of this protease aiming to derive common roles of AARE in cellular physiology, potentially in aging, but also highlight differences between species isoforms.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009903","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":"ECLIPSE mediates selective degradation of inner nuclear membrane protein in plants.","authors":"Enrico Calvanese, Min Jia, Olivia Xie, Yangnan Gu","doi":"10.1093/jxb/eraf167","DOIUrl":"https://doi.org/10.1093/jxb/eraf167","url":null,"abstract":"<p><p>The inner nuclear membrane (INM) hosts a unique set of membrane proteins essential for nuclear functions. Proteolytic removal of mislocalized or defective membrane proteins is of critical importance for maintaining the homeostasis and integrity of the INM. Previous studies revealed that INM protein degradation depends on a specialized ubiquitin-proteasome system termed INM-Associated Degradation (INMAD) in plants, requiring the CDC48 complex and the 26S proteasome for membrane protein retrotranslocation and destruction, respectively. However, adaptor proteins that link membrane substrates to the CDC48/proteasome degradation machinery remain missing in the pathway. Here, we report the discovery of ECLIPSE, a previously uncharacterized protein that may serve as such a molecular bridge in the degradation of the conserved INM protein SUN1. We demonstrate that ECLIPSE physically associates with CDC48 and exhibits strong transcriptional co-regulation with multiple established plant INMAD components. Mechanistically, ECLIPSE may act as an adaptor through its dual-domain architecture: its C-terminal PUB domain mediates direct interaction with CDC48, while its N-terminal Ubiquitin-Associated domain recognizes ubiquitinated INM substrates. Genetic and biochemical analyses further established that ECLIPSE is required for SUN1 protein degradation in Arabidopsis, supporting its role in the turnover of at least some inner nuclear membrane proteins in plants.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021983","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}
Raviraj M Kalunke, Ambika Pokhrel, Meenakshi Tetorya, James Godwin, Vishnu Sukumari Nath, Kirk J Czymmek, Dilip M Shah
{"title":"Modes of action and bio-fungicide potential of peptides derived from the bi-domain plant defensin MtDef5.","authors":"Raviraj M Kalunke, Ambika Pokhrel, Meenakshi Tetorya, James Godwin, Vishnu Sukumari Nath, Kirk J Czymmek, Dilip M Shah","doi":"10.1093/jxb/eraf166","DOIUrl":"https://doi.org/10.1093/jxb/eraf166","url":null,"abstract":"<p><p>The Medicago truncatula bi-domain defensin MtDef5 exhibits activity at sub-micromolar concentrations against some fungal pathogens. It is comprised of two single-domain defensins, MtDef5A and MtDef5B, connected with the linker peptide APKKVEP. MtDef5B exhibits greater antifungal potency compared to MtDef5A. We identified amino acid residues important for antifungal activity of MtDef5B and elucidated its modes of action (MoA). MtDef5B inhibited spore germination of Botrytis cinerea (Bc) at low micromolar concentrations. However, it did not inhibit spore germination of Colletotrichum gloeosporioides (Cg). MtDef5B permeabilized the plasma membrane, induced the production of reactive oxygen species, and localized to the nucleoli in Bc germlings. The carboxy-terminal MtDef5A-derived GMA5AC peptide was selected for mutagenesis because of its lower cationic charge than the corresponding MtDef5B-derived peptide. GMA5AC inhibited spore germination of Bc, but not of Cg. However, GMA5AC_V2, a variant of GMA5AC, inhibited spore germination of Cg and exhibited a multi-faceted MoA. Spray-application of GMA5AC_V2 on the leaves of pepper plants resulted in pre- and post-inoculation control of the gray mold disease. Furthermore, when applied topically on tomato fruits pre-inoculated with the pathogen Cg, this peptide reduced anthracnose disease symptoms. This study highlights the potential of short chain defensin-derived peptides for management of fungal diseases.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004824","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}
Leonardo Jo, Sara Buti, Mariana A S Artur, Rianne M C Kluck, Alex Cantó-Pastor, Siobhán M Brady, Kaisa Kajala
{"title":"Transcription factors SlMYB41, SlMYB92 and SlWRKY71 regulate gene expression in the tomato exodermis.","authors":"Leonardo Jo, Sara Buti, Mariana A S Artur, Rianne M C Kluck, Alex Cantó-Pastor, Siobhán M Brady, Kaisa Kajala","doi":"10.1093/jxb/eraf161","DOIUrl":"https://doi.org/10.1093/jxb/eraf161","url":null,"abstract":"<p><p>Root barrier cell types, like the endodermis and exodermis, are crucial for plant acclimation to environmental stresses. Deposition of suberin, a hydrophobic polymer, in these cell layers restricts the movement of molecules and plays a vital role in stress responses. This study investigates the role of SlMYB41, SlMYB92 and SlWRKY71 transcription factors (TFs) in regulating suberin biosynthesis in the tomato (Solanum lycopersicum) root exodermis by genetic perturbation. Genetic perturbation of these TFs altered exodermal suberin deposition patterns, indicating the SlMYBs as positive and SlWRKY71 negative regulators of suberization. RNA sequencing revealed a significant overlap between differentially expressed genes regulated by these TFs, suggesting a shared regulatory network. Gene set enrichment analyses highlighted their role in lipid and suberin biosynthesis as well as overrepresentation of exodermis-enriched transcripts. Furthermore, transactivation assays demonstrated that these two MYBs promote the expression of suberin-related genes, while SlWRKY71 represses them. These results indicate a complex antagonistic relationship, advancing our understanding of the regulatory mechanisms controlling exodermis suberization in tomato roots.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143994822","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":"Genetic diversity of leaf photosynthesis under fluctuating light conditions among temperate japonica rice varieties.","authors":"Kazuki Taniyoshi, Sotaro Honda, Airi Miyamoto, Naomi Asagi, Makoto Matsuoka, Wataru Yamori, Yu Tanaka, Shunsuke Adachi","doi":"10.1093/jxb/eraf083","DOIUrl":"https://doi.org/10.1093/jxb/eraf083","url":null,"abstract":"<p><p>Under field conditions, solar radiation on a crop canopy fluctuates according to clouds, wind, and self-shading. The slower response of photosynthesis compared with the rate of irradiation changes leads to loss of photosynthetic carbon gain. Although some genetic differences in the rate of photosynthetic induction have been reported, the diversity among rice varieties is largely unknown. Here we evaluated genetic variation in the response of photosynthesis to a step increase in light intensity among 166 temperate japonica varieties including landraces and modern varieties. Large genetic variation in photosynthetic induction and less evidence of improvement across modern breeding programmes were acknowledged. In the correlation analysis between physiological traits for all varieties, the efficiency of non-stomatal processes was the major factor affecting the rate of induction. The landrace Aikokumochi, which has intermediate photosynthetic capacity, showed rapid photosynthetic induction-eight times that of the slowest variety. This was attributed to smaller non-stomatal limitation in the initial phase of induction and smaller stomatal limitation in the later phase than in reference varieties. Aikokumochi also had a greater photosynthetic CO2 gain without reduced water use efficiency under repeated fluctuating light. These findings demonstrate the importance of genetic resources to improve photosynthesis while maintaining water use efficiency under fluctuating light conditions.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013959","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}
Isobella Revell, Peng Zhang, Chongmei Dong, William T Salter, Richard Trethowan
{"title":"Heterosis in wheat: mechanisms, benefits, and challenges in hybrid development.","authors":"Isobella Revell, Peng Zhang, Chongmei Dong, William T Salter, Richard Trethowan","doi":"10.1093/jxb/eraf159","DOIUrl":"https://doi.org/10.1093/jxb/eraf159","url":null,"abstract":"<p><p>Heterosis, or hybrid vigour, has been exploited by plant breeders and grain growers for more than a century, and open pollinated crops such as maize have been successfully commercialised. However, the full genetic potential of heterosis has yet to be realised and the fundamental mechanisms underlying this complex process are poorly understood. The challenges of hybrid seed production in self-pollinated crops, including cereals such as wheat and barley, have prevented the widespread exploitation of heterosis in these crops. Focussing on wheat, this review details current understanding of the genetic control of heterosis and explores the efficacy of different methods for producing F1 hybrids. We posit (1) that the mechanisms underlying heterosis are likely a combination of multiple or all current theories and (2) that the conversion of inbred crops like wheat into hybrid breeding systems can be further enhanced using a complete genic system, lessening the need for current, more complex hybrid production systems.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144039781","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}
Alana R O Chin, Arthur Gessler, Paula Guzmán-Delgado, Rubén D Manzanedo, Matthias Saurer, Janneke Hille Ris Lambers
{"title":"Rainwater uptake in conifer twigs: Five experiments tell a story of absorption, storage, and transport.","authors":"Alana R O Chin, Arthur Gessler, Paula Guzmán-Delgado, Rubén D Manzanedo, Matthias Saurer, Janneke Hille Ris Lambers","doi":"10.1093/jxb/eraf087","DOIUrl":"https://doi.org/10.1093/jxb/eraf087","url":null,"abstract":"<p><p>While evidence supports the idea that a portion of the many raindrops that fall onto a forest canopy may be directly absorbed by the twigs they lands on, we do not know how much is absorbed, how it enters the twig, or what internal path it might take on its way to the xylem. Using a diverse series of 5 experiments encompassing isotopic labeling, fluorescent tracers, rehydration kinetics, synchrotron-based X-ray tomographic microscopy, and thermal imaging, we follow the fate of rainwater from initial contact with the twig to its distribution to adjacent tissues. We provide conclusive, multi-pronged evidence of surface water-absorption into the xylem of year-old conifer twigs with incomplete bark development. Additionally, we demonstrate a surface capillary phase, mixed apoplastic and symplastic internal routes, and the strong influence of intercellular airspace as a hydraulic capacitor across multiple tissues. We show that twigs are capable of rapid, large-volume water absorption which may help trees take advantage of crown-wetting events and support the repair of hydraulic damage from frost and drought. Forecasting the impacts of climatic stress on different tree species will benefit from understanding the importance, and tissue-level specifics, of this critical water-acquisition pathway. Our works tells a detailed story of rain absorption and lays a foundation for future trait-based research into among-species differences in absorption capacity.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023408","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}