Maurice Koenig, Zarah Sorger, Shania Pin Yin Keh, Gunther Doehlemann, Johana C Misas Villamil
{"title":"Quantitative detection of the maize phytocytokine Zip1 utilizing ELISA.","authors":"Maurice Koenig, Zarah Sorger, Shania Pin Yin Keh, Gunther Doehlemann, Johana C Misas Villamil","doi":"10.1093/jxb/erae423","DOIUrl":"10.1093/jxb/erae423","url":null,"abstract":"<p><p>Plant signaling peptides, also known as phytocytokines, play a crucial role in cell-to-cell communication during plant development and immunity. The detection of small peptides in plant tissues is challenging and often relies on time-consuming and cost-intensive approaches. Here, we present an ELISA-based assay as a rapid and cost-effective method for the detection of naturally released peptides in plant tissues. Our ELISA-based method was developed to detect Zip1, a 17-amino-acid phytocytokine derived from Zea mays that elicits salicylic acid signaling in maize leaves. Using a custom peptide-antibody, we designed an experimental pipeline to achieve peptide specificity, selectivity, and sensitivity allowing the detection of the Zip1 peptide in complex biological samples. As a proof of concept, we first overexpressed the precursor molecule PROZIP1 in Nicotiana benthamiana and in transfected maize protoplasts and monitored the release of Zip1-containing peptides. In a second approach we treated maize leaves with salicylic acid to induce native PROZIP1 expression and processing. Using ELISA, we were able to quantify native Zip1 signals with a detection limit in the nanogram range, which allowed us to detect different Zip1-containing peptides in plant material. This method can be adapted for the detection and quantification of a variety of plant signaling peptides.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"299-311"},"PeriodicalIF":5.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11714748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824094","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":"Down-regulation of the rice HRS1 HOMOLOG3 transcriptional repressor gene due to N deficiency directly co-activates ammonium and phosphate transporter genes.","authors":"Mailun Yang, Yasuhito Sakuraba, Shuichi Yanagisawa","doi":"10.1093/jxb/erae440","DOIUrl":"10.1093/jxb/erae440","url":null,"abstract":"<p><p>Rice HRS1 HOMOLOG3 (OsHHO3) acts as a transcriptional repressor of AMMONIUM TRANSPORTER1 (OsAMT1) genes in rice; thus, reduced OsHHO3 expression in nitrogen (N)-deficient environments promotes ammonium uptake. In this study, we show that OsHHO3 also functions as a repressor of a specific subset of phosphate (Pi) transporter (PT) genes involved in the uptake and root-to-shoot translocation of Pi, including OsPT2, OsPT4, and OsPHO1;1. Disruption of OsHHO3 increased Pi uptake and Pi contents in shoots and roots, while overexpression of OsHHO3 caused the opposite effects. Furthermore, phosphorus (P) deficiency slightly decreased OsHHO3 expression, up-regulating a specific subset of PT genes. However, N deficiency was more effective than P deficiency in suppressing OsHHO3 expression in roots, and unlike N deficiency-dependent activation of PT genes under the control of OsHHO3, the P deficiency-dependent activation of OsAMT1 genes was minimal. Interestingly, the simultaneous deficiency of both N and P promoted the OsHHO3-regulated expression of PT genes more significantly than the deficiency of either N or P, but diminished the expression of genes regulated by OsPHR2, a master regulator of Pi starvation-responsive transcriptional activation. Phenotypic analysis revealed that the inactivation and overexpression of OsHHO3 improved and reduced plant growth, respectively, under N-deficient and P-deficient conditions. These results indicate that OsHHO3 regulates a specific subset of PT genes independently of OsPHR2-mediated regulation and plays a critical role in the adaptation to diverse N and P environments.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"461-477"},"PeriodicalIF":5.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11714757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521989","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}
Sara Bernardo, Elisa Marguerit, Nathalie Ollat, Gregory A Gambetta, Clément Saint Cast, Marina de Miguel
{"title":"Root system ideotypes: what is the potential for breeding drought-tolerant grapevine rootstocks?","authors":"Sara Bernardo, Elisa Marguerit, Nathalie Ollat, Gregory A Gambetta, Clément Saint Cast, Marina de Miguel","doi":"10.1093/jxb/eraf006","DOIUrl":"https://doi.org/10.1093/jxb/eraf006","url":null,"abstract":"<p><p>Adaptation to drought is one of the most important challenges for agriculture. The root system, and its integration with the soil, is fundamental in conferring drought tolerance. At the same time, it is extremely challenging to study. The result is that investigations aimed at increasing crop drought tolerance have mainly focused on above-ground traits, especially for perennial species. In this review, we explore the root trait syndromes that would constitute drought tolerant ideotypes, taking the example of grapevine as a model perennial grafted plant. We introduce and discuss the complexity of root trait interactions across different spatial and temporal scales considering their diversity, plasticity, and possible trade-offs. Finally, we review future approaches for discovering hidden root trait syndromes conferring drought tolerance, such as state-of-the-art root phenotyping technologies, the use of modeling as a tool to upscale root traits to the field, and new strategies to link genes to phenotypes. Together these integrated approaches can improve the breeding of drought tolerant grapevine rootstocks.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949854","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}
Raquel Álvarez-Urdiola, José Tomás Matus, Víctor Manuel González-Miguel, Martí Bernardo-Faura, José Luis Riechmann
{"title":"Chronology of transcriptome and proteome expression during early Arabidopsis flower development.","authors":"Raquel Álvarez-Urdiola, José Tomás Matus, Víctor Manuel González-Miguel, Martí Bernardo-Faura, José Luis Riechmann","doi":"10.1093/jxb/eraf005","DOIUrl":"https://doi.org/10.1093/jxb/eraf005","url":null,"abstract":"<p><p>The complex gene regulatory landscape underlying early flower development in Arabidopsis has been extensively studied through transcriptome profiling, and gene networks controlling floral organ development have been derived from the analyses of genome wide binding of key transcription factors. In contrast, the dynamic nature of the proteome during the flower development process is much less understood. In this study, we characterized the floral proteome at different stages during early flower development and correlated it with unbiased transcript expression data. Shotgun proteomics and transcript profiling were conducted using an APETALA1-based floral induction system. A specific analysis pipeline to process the time-course proteomics data was developed. In total, 8,924 proteins and 23,069 transcripts were identified. Co-expression analysis revealed that RNA-protein pairs clustered in various expression pattern modules. An overall positive correlation between RNA and protein level changes was observed, but subgroups of RNA/protein pairs with anticorrelated gene expression changes were also identified and found to be enriched in hormone responsive pathways. In addition, the RNA-seq dataset reported here further expanded the identification of genes whose expression changes during early flower development, and its combination with previously published AP1 ChIP-seq datasets allowed the identification of additional AP1 direct and high-confidence targets.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949851","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}
Na Ge, Jin-Shan Jia, Qing-Yan Wang, Chao-Lin Li, Min Huang, Jun-Wen Chen
{"title":"A genome-wide survey of DNA methylation reveals hyper-methylation regulates after-ripening and dormancy of recalcitrant Panax notoginseng seeds.","authors":"Na Ge, Jin-Shan Jia, Qing-Yan Wang, Chao-Lin Li, Min Huang, Jun-Wen Chen","doi":"10.1093/jxb/erae508","DOIUrl":"https://doi.org/10.1093/jxb/erae508","url":null,"abstract":"<p><p>DNA methylation plays a crucial role in regulating fruit ripening and seed development. It remains unknown about the dynamic characteristics of DNA methylation and its regulation mechanisms in morpho-physiological dormancy (MPD)-typed seeds with recalcitrant characteristics. The Panax notoginseng seeds are defined by the MPD and are characterized by a strong sensitivity to dehydration during the after-ripening process. We performed DNA methylomes, siRNA profiles, and transcriptomes of embryo and endosperm in P. notoginseng seeds at different after-ripening stages. Herein, we find that the hyper-methylation contributes to the increase in DNA methylation during the after-ripening process. The endosperm genome is hyper-methylated compared to the embryo genome. The hyper-methylation is caused by the high expression level of DNA methyltransferase PnCMT2 in the seeds. The hyper-methylation alters gene transcription levels to regulate the after-ripening and dormancy of recalcitrant seeds. For example, it inhibits the expression of genes in embryo development to make seeds maintain a dormant status. Together, our findings reveal an increase in DNA methylation and its vital driver in gene expression, and thus elucidate how hyper-methylation regulates the after-ripening in recalcitrant MPD-typed seeds. This work establishes a key role for epigenetics in regulating the dormancy of MPD-typed seeds with recalcitrant characteristics.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949846","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}
Melika L Missen, Martin G De Kauwe, Mark J Hovenden
{"title":"Increasing photosynthetic benefit with decreasing irrigation frequency in an Australian temperate pasture exposed to elevated carbon dioxide.","authors":"Melika L Missen, Martin G De Kauwe, Mark J Hovenden","doi":"10.1093/jxb/erae511","DOIUrl":"https://doi.org/10.1093/jxb/erae511","url":null,"abstract":"<p><p>Elevated atmospheric CO2 (e[CO2]) often enhances plant photosynthesis and improves water status. However, the effects of e[CO2] vary significantly and are believed to be influenced by water availability. With the future warmer climate expected to increase the frequency and severity of extreme rainfall, the response of plants to e[CO2] under changing precipitation patterns remains uncertain. We examined the effects of e[CO2] and different irrigation regimes on perennial ryegrass in a Free-Air CO2 Enrichment (FACE) experiment. Immediately after irrigation, the mean net photosynthetic rate was 21.2% higher under e[CO2] compared to ambient conditions. This benefit increased over time, reaching 31.3% higher as days since watering increased, indicating a substantial increase in photosynthetic benefit with longer intervals between watering. Mean stomatal conductance was 21% lower in ryegrass under e[CO2] immediately after irrigation compared to ambient plots. However, the reduction in stomatal conductance under e[CO2] decreased as the interval between irrigation events increased, showing no difference 7-10 days after an irrigation event. These results imply that plants benefit most from carbon fertilisation, assimilating relatively more carbon and losing less water, during periods with less frequent rainfall. These findings have significant implications for understanding leaf-level responses to climate change.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949853","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}
Toby Coombe-Tennant, Xiaoping Zhu, Shihua Wu, Gary J Loake
{"title":"Recent advances in paclitaxel biosynthesis and regulation.","authors":"Toby Coombe-Tennant, Xiaoping Zhu, Shihua Wu, Gary J Loake","doi":"10.1093/jxb/erae240","DOIUrl":"10.1093/jxb/erae240","url":null,"abstract":"<p><p>Paclitaxel (PTX) is a high value plant natural product derived from Taxus (yew) species. This plant specialized metabolite (PSM) and its derivatives constitute a cornerstone for the treatment of an increasing variety of cancers. New applications for PTX also continue to emerge, further promoting demand for this WHO-designated essential medicine. Here we review recent advances in our understanding of PTX biosynthesis and its cognate regulation, which have been enabled by the development of transcriptomic approaches and the recent sequencing and annotation of three Taxus genomes. Collectively, this has resulted in the elucidation of two functional gene sets for PTX biosynthesis, unlocking new potential for the use of heterologous hosts to produce PTX. Knowledge of the PTX pathway also provides a valuable resource for understanding the regulation of this key PSM. Epigenetic regulation of PSM in plant cell culture is a major concern for PTX production, given the loss of PSM production in long-term cell cultures. Recent developments aim to design tools for manipulating epigenetic regulation, potentially providing a means to reverse the silencing of PSM caused by DNA methylation. Exciting times clearly lie ahead for our understanding of this key PSM and improving its production potential.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"124-133"},"PeriodicalIF":5.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081748","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}
Ajwal Dsouza, Mike Dixon, Mukund Shukla, Thomas Graham
{"title":"Harnessing controlled-environment systems for enhanced production of medicinal plants.","authors":"Ajwal Dsouza, Mike Dixon, Mukund Shukla, Thomas Graham","doi":"10.1093/jxb/erae248","DOIUrl":"10.1093/jxb/erae248","url":null,"abstract":"<p><p>Medicinal plants are valued for their contributions to human health. However, the growing demand for medicinal plants and the concerns regarding their quality and sustainability have prompted the reassessment of conventional production practices. Controlled-environment cropping systems, such as vertical farms, offer a transformative approach to production of medicinal plants. By enabling precise control over environmental factors, such as light, carbon dioxide, temperature, humidity, nutrients, and airflow, controlled environments can improve the consistency, concentration, and yield of bioactive phytochemicals in medicinal plants. This review explores the potential of controlled-environment systems for enhancing production of medicinal plants. First, we describe how controlled environments can overcome the limitations of conventional production in improving the quality of medicinal plants. Next, we propose strategies based on plant physiology to manipulate environmental conditions for enhancing the levels of bioactive compounds in plants. These strategies include improving photosynthetic carbon assimilation, light spectrum signalling, purposeful stress elicitation, and chronoculture. We describe the underlying mechanisms and practical applications of these strategies. Finally, we highlight the major knowledge gaps and challenges that limit the application of controlled environments, and discuss future research directions.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"76-93"},"PeriodicalIF":5.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179810","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}
Ricarda Jost, Oliver Berkowitz, Amelia Pegg, Bhavna Hurgobin, Muluneh Tamiru-Oli, Matthew T Welling, Myrna A Deseo, Hannah Noorda, Filippa Brugliera, Mathew G Lewsey, Monika S Doblin, Antony Bacic, James Whelan
{"title":"Sink strength, nutrient allocation, cannabinoid yield, and associated transcript profiles vary in two drug-type Cannabis chemovars.","authors":"Ricarda Jost, Oliver Berkowitz, Amelia Pegg, Bhavna Hurgobin, Muluneh Tamiru-Oli, Matthew T Welling, Myrna A Deseo, Hannah Noorda, Filippa Brugliera, Mathew G Lewsey, Monika S Doblin, Antony Bacic, James Whelan","doi":"10.1093/jxb/erae367","DOIUrl":"10.1093/jxb/erae367","url":null,"abstract":"<p><p>Cannabis sativa L. is one of the oldest domesticated crops. Hemp-type cultivars, which predominantly produce non-intoxicating cannabidiol (CBD), have been selected for their fast growth, seed, and fibre production, while drug-type chemovars were bred for high accumulation of tetrahydrocannabinol (THC). We investigated how the generation of CBD-dominant chemovars by introgression of hemp- into drug-type Cannabis impacted plant performance. The THC-dominant chemovar showed superior sink strength, higher flower biomass, and demand-driven control of nutrient uptake. By contrast, the CBD-dominant chemovar hyperaccumulated phosphate in sink organs leading to reduced carbon and nitrogen assimilation in leaves, which limited flower biomass and cannabinoid yield. RNA-seq analyses determined organ- and chemovar-specific differences in expression of genes associated with nitrate and phosphate homeostasis as well as growth-regulating transcription factors that were correlated with measured traits. Among these were genes positively selected for during Cannabis domestication encoding an inhibitor of the phosphate starvation response, SPX DOMAIN GENE3, nitrate reductase, and two nitrate transporters. Altered nutrient sensing, acquisition, or distribution are likely a consequence of adaption to growth on marginal, low-nutrient-input lands in hemp. Our data provide evidence that such ancestral traits may become detrimental for female flower development and consequently overall CBD yield in protected cropping environments.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"152-174"},"PeriodicalIF":5.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120005","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}
Benjamin Wee Y, Oliver Berkowitz, James Whelan, Ricarda Jost
{"title":"Same, yet different: towards understanding nutrient use in hemp- and drug-type Cannabis.","authors":"Benjamin Wee Y, Oliver Berkowitz, James Whelan, Ricarda Jost","doi":"10.1093/jxb/erae362","DOIUrl":"10.1093/jxb/erae362","url":null,"abstract":"<p><p>Cannabis sativa L., one of the oldest cultivated crops, has a complex domestication history due to its diverse uses for fibre, seed, oil, and drugs, and its wide geographic distribution. This review explores how human selection has shaped the biology of hemp and drug-type Cannabis, focusing on acquisition and utilization of nitrogen and phosphorus, and how resulting changes in source-sink relations shape their contrasting phenology. Hemp has been optimized for rapid, slender growth and nutrient efficiency, whereas drug-type cultivars have been selected for compact growth with large phytocannabinoid-producing female inflorescences. Understanding these nutrient use and ontogenetic differences will enhance our general understanding of resource allocation in plants. Knowledge gained in comparison with other model species, such as tomato, rice, or Arabidopsis can help inform crop improvement and sustainability in the cannabis industry.</p>","PeriodicalId":15820,"journal":{"name":"Journal of Experimental Botany","volume":" ","pages":"94-108"},"PeriodicalIF":5.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046730","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}