{"title":"Before import: N-terminal acetylation at the interface of plastid protein targeting and proteostasis.","authors":"Pia M Möllenbeck, Sacha Baginsky","doi":"10.1093/jxb/erag481","DOIUrl":"https://doi.org/10.1093/jxb/erag481","url":null,"abstract":"<p><p>Most chloroplast proteins are synthesized in the cytosol as precursor proteins carrying N-terminal transit peptides that mediate post-translational import into the organelle. During this transient cytosolic phase, precursor proteins are exposed to the cellular N-terminal processing machinery, including methionine aminopeptidases and N-terminal acetyltransferases (NATs). Recent proteomic studies have provided direct evidence that plastid precursor proteins undergo N-terminal acetylation prior to import, establishing a previously unrecognized link between co-translational processing and plastid protein targeting. Here, we review current knowledge of N-terminal processing of plastid precursor proteins, including sequence determinants, NAT specificity, and experimental evidence for precursor acetylation in vivo. We discuss how precursor acetylation may influence precursor fate by affecting protein stability, import competence, and cytosolic quality-control pathways. Finally, we propose that the high prevalence of NatA-compatible plastid precursor proteins may reflect evolutionary constraints imposed on transit peptide architecture by organelle targeting and import. Understanding how N-terminal processing intersects with precursor protein targeting will provide new insights into the regulation of plastid biogenesis and cytosolic proteostasis in plants.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149074862","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}
Patrick Pascal Lehr, Victoria Gödde, Karsten Niehaus, Christian Zörb
{"title":"Nitrogen status defines grapevine metabolic response to sulfur deficiency.","authors":"Patrick Pascal Lehr, Victoria Gödde, Karsten Niehaus, Christian Zörb","doi":"10.1093/jxb/erag123","DOIUrl":"10.1093/jxb/erag123","url":null,"abstract":"<p><p>Sulfur is an essential macronutrient, yet its role in grapevine (Vitis vinifera L.) physiology is poorly understood. Following reduced atmospheric sulfur deposition, sulfur fertilization is increasingly required to prevent deficiencies, which are difficult to diagnose before they impair grapevine-and subsequent wine-quality. Therefore, the metabolic responses of grapevines to isolated and combined sulfur and nitrogen deficiencies were investigated. Using a non-targeted metabolomics and ionomics approach under controlled sulfur and nitrogen supplies, it was shown that isolated sulfur deficiency led to a massive accumulation of nitrogen-rich amino acids and activation of the gamma-aminobutyric acid shunt. This metabolic imbalance, and its disruptive effect on the concentration of other plant nutrients, was significantly alleviated under combined sulfur deficiency and low nitrogen, while additive effects also occurred. Sulfur deficiency uniquely induced a drastic increase in transpiration, significantly reducing intrinsic water use efficiency. We identified specific metabolic markers for each nutrient status and evaluated diagnostic indicators. The interaction between sulfur and nitrogen is important and demonstrates that adequate sulfate nutrition is essential for optimizing water use efficiency and metabolic balance, suggesting that nitrogen-management strategies should consider sulfur availability to ensure crop resilience in a changing climate.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6174-6192"},"PeriodicalIF":6.5,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147365606","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}
Isabeau Vanbuel, Sophie Hendrix, Céleste Maes, Lara Vanbriel, Kris Kunnen, Ann Cuypers
{"title":"Many roads lead to autophagy: the connection between sulfur metabolism and autophagy during metal stress in plants.","authors":"Isabeau Vanbuel, Sophie Hendrix, Céleste Maes, Lara Vanbriel, Kris Kunnen, Ann Cuypers","doi":"10.1093/jxb/erag211","DOIUrl":"10.1093/jxb/erag211","url":null,"abstract":"<p><p>During plant development and in response to stress conditions, autophagy contributes to the intracellular degradation of cellular components and subsequent nutrient recycling. As this process is highly connected to the nutrient status of the plant, autophagy also contributes to the mobilization of sulfur from source to sink tissues as well as the maintenance of primary sulfate assimilation. In turn, sulfur signals regulate autophagy, with sulfide (an intermediate of primary sulfate assimilation) exerting a repressive effect and sulfur deficiency having a stimulatory effect. In addition to a sulfur deficiency response in the plant resulting from low external sulfate availability, stresses such as metal exposure also perturb sulfur metabolism and can induce a 'functional sulfur deficiency' response through a surge in the production of thiol-rich metal chelators. As autophagy is increasingly linked to metal stress responses, this review proposes potential pathways through which metal-induced autophagy is linked to perturbations in sulfur metabolism, focusing on redox alterations and sucrose non-fermenting 1 (SNF1)-related kinase (SnRK)/target of rapamycin (TOR)-mediated nutrient signalling. Lastly, the connection between plant stress tolerance, autophagy and sulfur status is also discussed in terms of potential valorization strategies to maximize plant growth on metal-contaminated soils.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6132-6148"},"PeriodicalIF":6.5,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147816072","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":"Sulfur in dialogue with phosphorus, nitrogen, and iron: regulatory networks in plant nutrient homeostasis.","authors":"Afm Mohabubul Haque, Hideki Takahashi, Hatem Rouached","doi":"10.1093/jxb/erag119","DOIUrl":"10.1093/jxb/erag119","url":null,"abstract":"<p><p>Sulfur (S) is an essential macronutrient for plant growth and resilience. The S-amino acids cysteine (Cys) and methionine (Met) are indispensable for protein synthesis and structural integrity, as well as redox homeostasis and cofactor assembly. Over the past several decades, biochemical and molecular genetic studies demonstrated the core steps in sulfate uptake and assimilation pathways, while it has become increasingly evident that S homeostasis in plants cannot be understood in isolation. Robust and reciprocal regulatory interactions link S with phosphorus (P), nitrogen (N), and iron (Fe). Plants remodel membrane lipid compositions, replacing the phospholipids with sulfolipids under P deficiency. Cys/Met biosynthesis is coordinated with N metabolism. The Fe-S cluster assembly requires a balanced supply of Fe and S. These interactions are orchestrated through shared regulatory circuits and specific hub-regulatory transcription factors, including SULFUR LIMITATION 1, PHOSPHATE STARVATION RESPONSE 1, NIN-LIKE PROTEIN 7, and FER-LIKE IRON DEFICIENCY-INDUCED FACTOR. Comparative studies reveal both species-specific and evolutionarily conserved regulatory networks. This review focuses on mechanistic insights into the regulatory circuits revealed from studies with the model plant Arabidopsis thaliana, where the genetic and molecular resolution enabled detailed dissection of the signaling and regulatory networks. This review also highlights unresolved mechanistic gaps and provides insights into systems-level understanding and potential translational approaches that can be implemented to improve crop nutrient use efficiency and stress resilience.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6048-6061"},"PeriodicalIF":6.5,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147355346","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}
Agnieszka Sirko, Anna Wawrzyńska, Marcin Olszak, Justyna Piotrowska, Marzena Sieńko
{"title":"Hidden players in plant response to sulfur deficit and beyond: insights into the function of the proteins Sulfur Deficiency Induced and Response to Low Sulfur.","authors":"Agnieszka Sirko, Anna Wawrzyńska, Marcin Olszak, Justyna Piotrowska, Marzena Sieńko","doi":"10.1093/jxb/erag083","DOIUrl":"10.1093/jxb/erag083","url":null,"abstract":"<p><p>Sulfur is an essential macronutrient for plants, playing a central role in diverse metabolic processes. Under sulfur-deficient conditions, plants undergo extensive transcriptional reprogramming, which includes the induction of numerous genes encoding proteins of largely unknown function. Among these, two protein families have been studied more intensively: Sulfur Deficiency Induced (SDI) and Response to Low Sulfur (LSU). This review summarizes current experimental evidence on their involvement in sulfur assimilation, stress responses, and overall plant adaptation to sulfur scarcity. Special emphasis is placed on the LSU family, where recent evidence suggests that the function of these proteins extends beyond sulfur starvation responses, pointing to broader roles in plant growth, development, and resilience to diverse stresses.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6023-6034"},"PeriodicalIF":6.5,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146201803","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}
Nay Chi Khin, Melanie Carmody, Brett D Schwartz, Michael Dlugosch, Suyan Yee, Marten Moore, Michael Gardiner, Li Lynn Tan, Colin Jackson, Ben Corry, Lara R Malins, Barry Pogson, Kai Xun Chan
{"title":"High-throughput screening and structure-guided design of small molecules enable modulation of SAL-PAP stress signaling.","authors":"Nay Chi Khin, Melanie Carmody, Brett D Schwartz, Michael Dlugosch, Suyan Yee, Marten Moore, Michael Gardiner, Li Lynn Tan, Colin Jackson, Ben Corry, Lara R Malins, Barry Pogson, Kai Xun Chan","doi":"10.1093/jxb/erag376","DOIUrl":"10.1093/jxb/erag376","url":null,"abstract":"<p><p>Chloroplasts sense environmental stress and activate chloroplast-to-nucleus retrograde signalling, reprogramming nuclear gene expression for plant acclimation. One such pathway is regulated by the phosphatase, SAL, which hydrolyses the nucleotide signal 3'-phosphoadenosine 5'-phosphate (PAP), a by-product of secondary sulfur metabolism. In Arabidopsis thaliana, genetic loss of AtSAL1 elevates PAP and enhances stress tolerance but causes pleiotropic growth defects. To uncouple stress signalling from genetic pleiotropy, we conducted a high-throughput in vitro screen of 13 000 small molecules and identified V20, a competitive inhibitor of AtSAL1 with 3-fold greater potency than the known Li+ inhibitor. Structural analoguing of V20 and biochemical assays defined key pharmacophore features required for inhibition. Accelerated molecular dynamics simulations revealed two previously uncharacterized V20-binding pockets adjacent to the catalytic site. V20 binding induces conformational changes which restrict substrate access to the catalytic site. Exogenous application of V20 to Arabidopsis led to increased PAP accumulation, activated PAP-responsive gene expression, and enhanced oxidative tolerance. Our findings reveal new insights into the regulatory domains of SAL enzymatic activity for control of PAP-mediated signalling and establish a proof-of-concept for targeted chemical modulation of SAL activity, which offers novel strategies to selectively manipulate oxidative stress signalling and sulfur metabolism in plants.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"6276-6294"},"PeriodicalIF":6.5,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148591982","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":"Thermal regulation shapes the coordination of stomatal conductance, transpiration, and photosynthesis in rice.","authors":"Yanchao Zhao, Jingwei Wu, Victor Flo, Jing Wang, Qisen Zhang, Maurizio Mencuccini","doi":"10.1093/jxb/erag484","DOIUrl":"https://doi.org/10.1093/jxb/erag484","url":null,"abstract":"<p><p>Heat-stress driven by global warming alters rice (Oryza sativa) water-use dynamics. To assess adaptive water-use strategies under elevated air temperature, we conducted a three-year whole-season experiment in natural light climate chambers with ambient, +1 °C, +2 °C, and +5 °C warming treatments. Stomatal conductance (gs), transpiration rate (E), net photosynthetic rate (An) and leaf developmental dynamics were continuously measured across growth stages. Above the photosynthetic optimum leaf temperature (Tleaf-opt-An = 30.8 °C), An declined while gs increased. The increase in gs accelerated beyond a critical threshold (Tleaf-crit = 34.2). This stomatal-photosynthetic decoupling was associated with enhanced transpiration and evaporative cooling. During the reproductive stage, heat stress constrained grain-filling sink capacity and delayed leaf senescence, sustaining higher An, gs and E. Rice exhibits heat-induced shifts in the coordination among carbon assimilation, stomatal behaviour, and water use, while source-sink dynamics under heat-stress further modulated carbon assimilation and water consumption. Incorporating these mechanisms into land surface models is essential for more reliable predictions under global warming scenarios.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069056","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}
Abhishek Roychowdhury, Akash, Rajat Srivastava, Vishal, Martin Cerny, Pavel Kerchev, Rahul Kumar
{"title":"A tomato purple acid phosphatase SlPAP26b rewires tissue-specific Pi remobilization through differential perturbation of SlPHL1-SlSPX2 levels.","authors":"Abhishek Roychowdhury, Akash, Rajat Srivastava, Vishal, Martin Cerny, Pavel Kerchev, Rahul Kumar","doi":"10.1093/jxb/erag465","DOIUrl":"https://doi.org/10.1093/jxb/erag465","url":null,"abstract":"<p><p>Acid phosphatases, both intracellular and secretory, play a crucial role in maintaining phosphate (Pi) homeostasis in plants. Using an integrated omics approach in Pi-deficient tomato seedlings, we identified SlPAP26b as a prominent candidate potentially involved in Pi remobilization from senescing to developing tissues, supported by its strong transcript accumulation in leaves and roots and pronounced induction during leaf senescence. Both SlPHR1 and SlPHL1, the two main tomato MYB-CC domain transcription factors of the Pi starvation response, directly activated the transcription of SlPAP26b by binding to the P1BS element in its promoter. Functional characterization revealed that silencing of SlPAP26b leads to stunted shoot growth and reduced intracellular acid phosphatase activity. Tracer studies using radioactive P (γ-32P-ATP) confirmed impaired Pi translocation from older to younger leaves, resulting in lower Pi levels in young tissues even under Pi-sufficient conditions in the silenced seedlings. The protein abundance of SlSPX2, a negative regulator of SlPHL1, was markedly reduced in SlPAP26b-silenced seedlings, accompanied by a corresponding increase in SlPHL1 protein abundance. Notably, SlPAP26b silencing reduced SlSPX2 but increased SlPHL1 protein accumulation, accompanied by elevated expression of several Pi starvation-induced (PSI) genes in younger leaves and roots, indicating the misregulated activation of the Pi starvation response (PSR) even under Pi sufficiency. Collectively, these findings identify a previously uncharacterized function of SlPAP26b in mediating tissue-specific Pi remobilization by selectively modulating the SlSPX2-SlPHL1 regulatory module, thereby advancing our understanding of the molecular mechanisms underlying Pi homeostasis in plants.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149061901","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}
Luca Bianco, Nicola Busatto, Mirko Moser, Diego Micheletti, Lorenzo Spina, Michela Troggio, Stefano Piazza, Fabrizio Costa, Paolo Fontana
{"title":"Haplotype-specific analyses in apple: insights from 'Golden Delicious'.","authors":"Luca Bianco, Nicola Busatto, Mirko Moser, Diego Micheletti, Lorenzo Spina, Michela Troggio, Stefano Piazza, Fabrizio Costa, Paolo Fontana","doi":"10.1093/jxb/erag478","DOIUrl":"https://doi.org/10.1093/jxb/erag478","url":null,"abstract":"<p><p>Apple is one of the major cultivated fruit crops in temperate regions. To better support breeding programs and facilitate the development of improved cultivars, we generated a new haplotype-resolved and phased version of the 'Golden Delicious' genome, one of the founders of many modern apple lineages. The phased assembly features the separation of the two haplotypes, with a total size of 647.3 Mb and 649.2 Mb, respectively. The phasing was accurately validated with 10,321 specific Single Nucleotide Polymorphisms (SNPs). Telomere-to-telomere continuity was verified by the analysis of telomeric sequence composition at the end of each chromosome. Gene prediction identified a total of 45,116 genes in haplotype 1 and 45,063 genes in haplotype 2. A pangenome analysis employing 6 haplotype resolved genomes identified both common and unique gene families. The availability of a phased genome enabled the assessment of genome-wide allelic specific expression. Our case study, focusing on Md-PG1 (a key regulator of fruit softening), revealed that the allele present on haplotype 2 (GDH2-10g24673) was the dominant contributor to total gene expression. In addition, the phased genome also showed specific miRNA chromosomal distribution patterns, as well as a distinct methylation profile. Altogether, these genomic resources provide new insights into the allelic regulation of key agronomic traits and represent a valuable tool to accelerate apple breeding.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149061911","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}
Manuela Jurca, Johan Sjölander, Bertold Mariën, Rajesh Kumar Singh, Alexander Vergara, Jun Yu, Thomas Moritz, Maria E Eriksson
{"title":"Biotechnological adaptation of high-yielding, gibberellin-overproducing Populus trees to seasonal growth patterns.","authors":"Manuela Jurca, Johan Sjölander, Bertold Mariën, Rajesh Kumar Singh, Alexander Vergara, Jun Yu, Thomas Moritz, Maria E Eriksson","doi":"10.1093/jxb/erag483","DOIUrl":"https://doi.org/10.1093/jxb/erag483","url":null,"abstract":"<p><p>Tree growth is central to both terrestrial ecology and the forestry industry. Biotechnology for inducing the overproduction of phytohormones such as gibberellins (GAs) is a powerful tool for improving tree yield and wood properties. Augumentation of GAs in trees in temperate and boreal regions, however, prevents the induction of vegetative dormancy, which results in reduced yield and tree loss over time. Hybrid Populus trees (Populus tremula × P. tremuloides; Ptt) use an internal circadian clock to synchronise their daily metabolism and seasonal growth with predictable light and temperature changes in their local environment. This study focused on modulating GA production in Populus to demonstrate the importance of seasonal growth adaptation. Levels of bioactive GAs were modulated in transgenic trees using the endogenous D-TYPE CYCLIN 3;1 promoter (pPttCYCD3), which is regulated by the circadian clock component LATE ELONGATED HYPOCOTYL 2 (PttLHY2). This modulation resulted in both high yield and seasonal growth adaptation. Such work paves the way for the precision breeding of trees with increased yield that are adapted to local climate conditions.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149039091","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}