Marie Le Naour--Vernet, Mounia Lahfa, Josephine H. R. Maidment, André Padilla, Christian Roumestand, Karine de Guillen, Thomas Kroj, Stella Césari
Phytopathogenic fungi cause enormous yield losses in many crops, threatening both agricultural production and global food security. To infect plants, they secrete effectors targeting various cellular processes in the host. Putative effector genes are numerous in fungal genomes, and they generally encode proteins with no sequence homology to each other or to other known proteins or domains. Recent studies have elucidated and predicted three-dimensional structures of effectors from a wide diversity of plant pathogenic fungi, revealing a limited number of conserved folds. Effectors with very diverse amino acid sequences can thereby be grouped into families based on structural homology. Some structural families are conserved in many different fungi, and some are expanded in specific fungal taxa. Here, we describe the features of these structural families and discuss recent advances in predicting new structural families. We highlight the contribution of structural analyses to deepen our understanding of the function and evolution of fungal effectors. We also discuss prospects offered by advances in structural modeling for predicting and studying the virulence targets of fungal effectors in plants.
{"title":"Structure-guided insights into the biology of fungal effectors","authors":"Marie Le Naour--Vernet, Mounia Lahfa, Josephine H. R. Maidment, André Padilla, Christian Roumestand, Karine de Guillen, Thomas Kroj, Stella Césari","doi":"10.1111/nph.70075","DOIUrl":"https://doi.org/10.1111/nph.70075","url":null,"abstract":"Phytopathogenic fungi cause enormous yield losses in many crops, threatening both agricultural production and global food security. To infect plants, they secrete effectors targeting various cellular processes in the host. Putative effector genes are numerous in fungal genomes, and they generally encode proteins with no sequence homology to each other or to other known proteins or domains. Recent studies have elucidated and predicted three-dimensional structures of effectors from a wide diversity of plant pathogenic fungi, revealing a limited number of conserved folds. Effectors with very diverse amino acid sequences can thereby be grouped into families based on structural homology. Some structural families are conserved in many different fungi, and some are expanded in specific fungal taxa. Here, we describe the features of these structural families and discuss recent advances in predicting new structural families. We highlight the contribution of structural analyses to deepen our understanding of the function and evolution of fungal effectors. We also discuss prospects offered by advances in structural modeling for predicting and studying the virulence targets of fungal effectors in plants.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"35 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143695622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xue Bai, ShengYang Wu, Ai‐Ning Bai, Yu‐Meng Zhang, Yan Zhang, Xue‐Feng Yao, Tao Yang, Meng‐Meng Chen, Jin‐Lei Liu, Lei Li, Yao Zhou, Chun‐Ming Liu
SummaryMost rice varieties are able to grow in red high‐Fe soil, but the underlying mechanism remains elusive.Through forward genetic screening, we identified a red soil‐sensitive‐1 (rss1) mutant that exhibited severely retarded growth when grown in red soil but showed no evident phenotype in cinnamon soil.Under the red soil/high‐Fe conditions, rss1 exhibited increased Fe but decreased copper (Cu) concentrations in both roots and shoots, and the rss1 phenotype was partially rescued by Cu supplement. RSS1 encodes an OsSPL9 transcription factor that is expressed in pericycle cells and parenchyma cells surrounding xylem in roots. Under high‐Fe conditions, OsSPL9 activated expression of Cu transporters, including OsYSL16, OsCOPT1, and OsCOPT5 by binding to their promoters, and OsYSL16 overexpression partially rescued rss1 defects.We thus propose that OsSPL9 overcomes high‐Fe imposed Cu deficiency by activating the expressions of Cu transporter genes, allowing rice to adapt to red soil.
{"title":"OsSPL9 promotes Cu uptake and translocation in rice grown in high‐Fe red soil","authors":"Xue Bai, ShengYang Wu, Ai‐Ning Bai, Yu‐Meng Zhang, Yan Zhang, Xue‐Feng Yao, Tao Yang, Meng‐Meng Chen, Jin‐Lei Liu, Lei Li, Yao Zhou, Chun‐Ming Liu","doi":"10.1111/nph.70074","DOIUrl":"https://doi.org/10.1111/nph.70074","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Most rice varieties are able to grow in red high‐Fe soil, but the underlying mechanism remains elusive.</jats:list-item> <jats:list-item>Through forward genetic screening, we identified a <jats:italic>red soil‐sensitive</jats:italic>‐<jats:italic>1</jats:italic> (<jats:italic>rss1</jats:italic>) mutant that exhibited severely retarded growth when grown in red soil but showed no evident phenotype in cinnamon soil.</jats:list-item> <jats:list-item>Under the red soil/high‐Fe conditions, <jats:italic>rss1</jats:italic> exhibited increased Fe but decreased copper (Cu) concentrations in both roots and shoots, and the <jats:italic>rss1</jats:italic> phenotype was partially rescued by Cu supplement. <jats:italic>RSS1</jats:italic> encodes an <jats:italic>OsSPL9</jats:italic> transcription factor that is expressed in pericycle cells and parenchyma cells surrounding xylem in roots. Under high‐Fe conditions, OsSPL9 activated expression of Cu transporters, including <jats:italic>OsYSL16</jats:italic>, <jats:italic>OsCOPT1</jats:italic>, and <jats:italic>OsCOPT5</jats:italic> by binding to their promoters, and <jats:italic>OsYSL16</jats:italic> overexpression partially rescued <jats:italic>rss1</jats:italic> defects.</jats:list-item> <jats:list-item>We thus propose that OsSPL9 overcomes high‐Fe imposed Cu deficiency by activating the expressions of Cu transporter genes, allowing rice to adapt to red soil.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"28 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carboxysomes are self-assembled bacterial microcompartments (BMCs) that encapsulate the enzymes RuBisCO and carbonic anhydrase into a proteinaceous shell, enhancing the efficiency of photosynthetic carbon fixation. The chaperone CcmS was reported to participate in the assembly of β-carboxysomes; however, the underlying molecular mechanism remains elusive.
We report the crystal structure of CcmS from Synechocystis sp. PCC 6803, revealing a monomer of α/β fold. Moreover, its complex structures with two types of BMC hexamers, CcmK1 homohexamer and CcmK1-CcmK2 heterohexamer, reveal a same pattern of CcmS binding to the featured C-terminal segment of CcmK1.
Upon binding to CcmS, this C-terminal segment of CcmK1 is folded into an amphipathic α-helix protruding outward that might function as a hinge to crosslink adjacent BMC-H hexamers, thereby facilitating concerted and precise assembly of the β-carboxysome shell. Deletion of the ccmS gene or the 8-residue C-terminal coding region of ccmK1 resulted in the formation of aberrant and fewer carboxysomes, suppressed photosynthetic capacity in Synechocystis sp. PCC 6803.
These findings enable us to propose a putative model for the chaperone-assisted assembly of β-carboxysome shell and provide clues for the design and engineering of efficient carbon fixation machinery.
{"title":"Assembly mechanism of the β-carboxysome shell mediated by the chaperone CcmS","authors":"Jing Li, Jia-Xin Deng, Xin Chen, Bo Li, Bo-Rui Li, Zhong-Liang Zhu, Jiexi Liu, Yuxing Chen, Hualing Mi, Cong-Zhao Zhou, Yong-Liang Jiang","doi":"10.1111/nph.70086","DOIUrl":"https://doi.org/10.1111/nph.70086","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Carboxysomes are self-assembled bacterial microcompartments (BMCs) that encapsulate the enzymes RuBisCO and carbonic anhydrase into a proteinaceous shell, enhancing the efficiency of photosynthetic carbon fixation. The chaperone CcmS was reported to participate in the assembly of β-carboxysomes; however, the underlying molecular mechanism remains elusive.</li>\u0000<li>We report the crystal structure of CcmS from <i>Synechocystis</i> sp. PCC 6803, revealing a monomer of α/β fold. Moreover, its complex structures with two types of BMC hexamers, CcmK1 homohexamer and CcmK1-CcmK2 heterohexamer, reveal a same pattern of CcmS binding to the featured C-terminal segment of CcmK1.</li>\u0000<li>Upon binding to CcmS, this C-terminal segment of CcmK1 is folded into an amphipathic α-helix protruding outward that might function as a hinge to crosslink adjacent BMC-H hexamers, thereby facilitating concerted and precise assembly of the β-carboxysome shell. Deletion of the <i>ccmS</i> gene or the 8-residue C-terminal coding region of <i>ccmK1</i> resulted in the formation of aberrant and fewer carboxysomes, suppressed photosynthetic capacity in <i>Synechocystis</i> sp. PCC 6803.</li>\u0000<li>These findings enable us to propose a putative model for the chaperone-assisted assembly of β-carboxysome shell and provide clues for the design and engineering of efficient carbon fixation machinery.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"183 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alissar Cheaib, Jeff Chieppa, Evan A. Perkowski, Nicholas G. Smith
SummaryNatural selection favors growth by selecting a combination of plant traits that maximize photosynthetic CO2 assimilation at the lowest combined carbon costs of resource acquisition and use. We quantified how soil nutrient availability, plant nutrient acquisition strategies, and aridity modulate the variability in plant costs of nutrient acquisition relative to water acquisition (β).We used an eco‐evolutionary optimality framework and a global carbon isotope dataset to quantify β.Under low soil nitrogen‐to‐carbon (N : C) ratios, a mining strategy (symbioses with ectomycorrhizal and ericoid mycorrhizal fungi) reduced β by mining organic nitrogen, compared with a scavenging strategy (symbioses with arbuscular mycorrhizal fungi). Conversely, under high N : C ratios, scavenging strategies reduced β by effectively scavenging soluble nitrogen, compared with mining strategies. N2‐fixing plants did not exhibit reduced β under low N : C ratios compared with non‐N2‐fixing plants. Moisture increased β only in plants using a scavenging strategy, reflecting direct impacts of aridity on the carbon costs of maintaining transpiration in these plants. Nitrogen and phosphorus colimitation further modulated β.Our findings provide a framework for simulating the variability of plant economics due to plant nutrient acquisition strategies in earth system models.
{"title":"Soil resource acquisition strategy modulates global plant nutrient and water economics","authors":"Alissar Cheaib, Jeff Chieppa, Evan A. Perkowski, Nicholas G. Smith","doi":"10.1111/nph.70087","DOIUrl":"https://doi.org/10.1111/nph.70087","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Natural selection favors growth by selecting a combination of plant traits that maximize photosynthetic CO<jats:sub>2</jats:sub> assimilation at the lowest combined carbon costs of resource acquisition and use. We quantified how soil nutrient availability, plant nutrient acquisition strategies, and aridity modulate the variability in plant costs of nutrient acquisition relative to water acquisition (β).</jats:list-item> <jats:list-item>We used an eco‐evolutionary optimality framework and a global carbon isotope dataset to quantify β.</jats:list-item> <jats:list-item>Under low soil nitrogen‐to‐carbon (N : C) ratios, a mining strategy (symbioses with ectomycorrhizal and ericoid mycorrhizal fungi) reduced β by mining organic nitrogen, compared with a scavenging strategy (symbioses with arbuscular mycorrhizal fungi). Conversely, under high N : C ratios, scavenging strategies reduced β by effectively scavenging soluble nitrogen, compared with mining strategies. N<jats:sub>2</jats:sub>‐fixing plants did not exhibit reduced β under low N : C ratios compared with non‐N<jats:sub>2</jats:sub>‐fixing plants. Moisture increased β only in plants using a scavenging strategy, reflecting direct impacts of aridity on the carbon costs of maintaining transpiration in these plants. Nitrogen and phosphorus colimitation further modulated β.</jats:list-item> <jats:list-item>Our findings provide a framework for simulating the variability of plant economics due to plant nutrient acquisition strategies in earth system models.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"57 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Emmanuel Tergemina, Shifa Ansari, David E. Salt, Angela M. Hancock
<h2> Introduction</h2><p>Magnesium (Mg) is an essential nutrient in living organisms. In humans, Mg serves as a cofactor in over 300 enzymatic reactions and as a counter-ion for ATP (Jahnen-Dechent & Ketteler, <span>2012</span>). Mg influences muscle, nerve, cardiac, and endocrine functions (Jahnen-Dechent & Ketteler, <span>2012</span>; Fiorentini <i>et al</i>., <span>2021</span>). A substantial proportion of people in developed countries are at risk of Mg deficiency, partly due to the unintended consequences of the green revolution, which promoted fertilization with a combination of nitrogen (N), phosphorus (P), and potassium (K). Consequently, farmers have tended to prioritize these three-component fertilizers to increase crop yield and growth, resulting in soils depleted in secondary elements such as Mg (Guo <i>et al</i>., <span>2016</span>). However, since potassium inhibits the absorption of Mg, the standardization of NPK supplementation resulted in a widespread reduction in Mg in crops. Although plants represent the principal source of Mg for humans, Mg has received comparatively little attention in agriculture and has thus been referred to as a ‘forgotten element’ (Cakmak & Yazİcİ, <span>2010</span>).</p><p>Mg deficiency in plants restricts their growth and productivity (Aitken <i>et al</i>., <span>1999</span>; Guo <i>et al</i>., <span>2016</span>), primarily due to its essential role in photosynthesis. This is because Mg is the central element of Chl and acts as an activator of enzymes involved in photosynthetic CO<sub>2</sub> fixation (Shaul, <span>2002</span>; Hawkesford <i>et al</i>., <span>2012</span>). Typical plant responses to Mg deficiency include sugar accumulation in leaf tissues and leaf interveinal chlorosis on older leaves, leading to impairments in plant growth and yield (Hermans & Verbruggen, <span>2005</span>; Römheld, <span>2012</span>). Therefore, understanding the factors that impact Mg accumulation in plants has important implications for agriculture and human nutrition.</p><p>Mg acquisition in plants depends on its abundance and availability in soils. The abundance of Mg in soils is highly dependent on the parental material from which the soil develops and anthropogenic factors such as agricultural intensity. Mg availability depends on various edaphic factors, including soil pH, cation competition, cation exchange capacity, and environmental factors, including precipitation, temperature, and atmospheric carbon dioxide (CO<sub>2</sub>) levels (Mesić <i>et al</i>., <span>2007</span>; Sun <i>et al</i>., <span>2013</span>; Loladze, <span>2014</span>). Notably, Mg binds weakly to soil colloids due to its large hydrated radius, leading to its susceptibility to leaching (Maguire & Cowan, <span>2002</span>; Gransee & Führs, <span>2013</span>). This susceptibility is particularly pronounced in acidic soils with reduced cation exchange capacity (Aitken <i>et al</i>., <span>1999</span>; Grzebisz, <span
{"title":"Multiple independent MGR5 alleles contribute to a clinal pattern in leaf magnesium across the distribution of Arabidopsis thaliana","authors":"Emmanuel Tergemina, Shifa Ansari, David E. Salt, Angela M. Hancock","doi":"10.1111/nph.70069","DOIUrl":"https://doi.org/10.1111/nph.70069","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Magnesium (Mg) is an essential nutrient in living organisms. In humans, Mg serves as a cofactor in over 300 enzymatic reactions and as a counter-ion for ATP (Jahnen-Dechent & Ketteler, <span>2012</span>). Mg influences muscle, nerve, cardiac, and endocrine functions (Jahnen-Dechent & Ketteler, <span>2012</span>; Fiorentini <i>et al</i>., <span>2021</span>). A substantial proportion of people in developed countries are at risk of Mg deficiency, partly due to the unintended consequences of the green revolution, which promoted fertilization with a combination of nitrogen (N), phosphorus (P), and potassium (K). Consequently, farmers have tended to prioritize these three-component fertilizers to increase crop yield and growth, resulting in soils depleted in secondary elements such as Mg (Guo <i>et al</i>., <span>2016</span>). However, since potassium inhibits the absorption of Mg, the standardization of NPK supplementation resulted in a widespread reduction in Mg in crops. Although plants represent the principal source of Mg for humans, Mg has received comparatively little attention in agriculture and has thus been referred to as a ‘forgotten element’ (Cakmak & Yazİcİ, <span>2010</span>).</p>\u0000<p>Mg deficiency in plants restricts their growth and productivity (Aitken <i>et al</i>., <span>1999</span>; Guo <i>et al</i>., <span>2016</span>), primarily due to its essential role in photosynthesis. This is because Mg is the central element of Chl and acts as an activator of enzymes involved in photosynthetic CO<sub>2</sub> fixation (Shaul, <span>2002</span>; Hawkesford <i>et al</i>., <span>2012</span>). Typical plant responses to Mg deficiency include sugar accumulation in leaf tissues and leaf interveinal chlorosis on older leaves, leading to impairments in plant growth and yield (Hermans & Verbruggen, <span>2005</span>; Römheld, <span>2012</span>). Therefore, understanding the factors that impact Mg accumulation in plants has important implications for agriculture and human nutrition.</p>\u0000<p>Mg acquisition in plants depends on its abundance and availability in soils. The abundance of Mg in soils is highly dependent on the parental material from which the soil develops and anthropogenic factors such as agricultural intensity. Mg availability depends on various edaphic factors, including soil pH, cation competition, cation exchange capacity, and environmental factors, including precipitation, temperature, and atmospheric carbon dioxide (CO<sub>2</sub>) levels (Mesić <i>et al</i>., <span>2007</span>; Sun <i>et al</i>., <span>2013</span>; Loladze, <span>2014</span>). Notably, Mg binds weakly to soil colloids due to its large hydrated radius, leading to its susceptibility to leaching (Maguire & Cowan, <span>2002</span>; Gransee & Führs, <span>2013</span>). This susceptibility is particularly pronounced in acidic soils with reduced cation exchange capacity (Aitken <i>et al</i>., <span>1999</span>; Grzebisz, <span","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"71 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<div>While glasshouse-grown plants benefit from controlled environments, the majority of plants in the world are directly exposed to continuous changes in ambient temperatures. In 2024, the global surface temperature was 1.28°C above the 1951–1980 average (Bardan, <span>2025</span>), eclipsing the previous record set in 2023 (Esper <i>et al</i>., <span>2024</span>). The Intergovernmental Panel on Climate Change reports the likelihood of a consistent trajectory of rising temperature, although projections vary in magnitude under different scenarios (Masson-Delmotte <i>et al</i>., <span>2021</span>). Rising temperatures along with extreme weather events will significantly challenge the survival of wild plant populations and global agricultural stability. Understanding plant metabolic responses to temperature changes at a metabolic level is critical for engineering climate-resilient plants. Recently published in <i>New Phytologist</i>, Wendering <i>et al</i>. (<span>2025</span>; doi: 10.1111/nph.20420) present the first enzyme-constrained, genome-scale metabolic model of <i>Arabidopsis thaliana</i>. By integrating temperature-dependent constraints on enzyme kinetics, protein content, and photosynthetic capacity, this model not only advances our understanding of how plant metabolism responds to thermal stress at a systemic level but also provides a valuable framework for identifying metabolic and genetic targets to enhance temperature resistance, which could apply to crops. Furthermore, such insights may also help to preserve wild plant species facing climate-driven extinction risks (Nievola <i>et al</i>., <span>2017</span>). <blockquote><p><i>By integrating thermal proteomics experimental data with a machine learning algorithm, this hybrid parameter estimation strategy resolves a critical limitation in the development of large-scale models</i>…</p><div></div></blockquote></div><p>Plants have a limited capacity to regulate their canopy temperature (Guo <i>et al</i>., <span>2023</span>), which means that all internal metabolic reactions are influenced by external temperature fluctuations. Research on signaling transduction, epigenetic regulation, transcriptional networks, and post-translational regulation of heat and cold stress has gained significant attention (Ohama <i>et al</i>., <span>2017</span>; Ding & Yang, <span>2022</span>). However, responses to temperature changes in plants are initially observed at the metabolic level, with subsequent changes in gene expression to restore homeostasis (Casal & Balasubramanian, <span>2019</span>).</p><p>Predicting how temperature fluctuations affect overall plant metabolism remains a challenge because the direct temperature effects on individual metabolic enzymes are often not well defined quantitatively. To overcome this challenge, the authors have developed the <i>ecAraCore</i> model, which is an enzyme-constrained extension of the AraCore model (Arnold & Nikoloski, <span>2014</span>). The
{"title":"Unlocking plant metabolic resilience: how enzyme-constrained metabolic models illuminate thermal responses","authors":"Yu Wang","doi":"10.1111/nph.70100","DOIUrl":"https://doi.org/10.1111/nph.70100","url":null,"abstract":"<div>While glasshouse-grown plants benefit from controlled environments, the majority of plants in the world are directly exposed to continuous changes in ambient temperatures. In 2024, the global surface temperature was 1.28°C above the 1951–1980 average (Bardan, <span>2025</span>), eclipsing the previous record set in 2023 (Esper <i>et al</i>., <span>2024</span>). The Intergovernmental Panel on Climate Change reports the likelihood of a consistent trajectory of rising temperature, although projections vary in magnitude under different scenarios (Masson-Delmotte <i>et al</i>., <span>2021</span>). Rising temperatures along with extreme weather events will significantly challenge the survival of wild plant populations and global agricultural stability. Understanding plant metabolic responses to temperature changes at a metabolic level is critical for engineering climate-resilient plants. Recently published in <i>New Phytologist</i>, Wendering <i>et al</i>. (<span>2025</span>; doi: 10.1111/nph.20420) present the first enzyme-constrained, genome-scale metabolic model of <i>Arabidopsis thaliana</i>. By integrating temperature-dependent constraints on enzyme kinetics, protein content, and photosynthetic capacity, this model not only advances our understanding of how plant metabolism responds to thermal stress at a systemic level but also provides a valuable framework for identifying metabolic and genetic targets to enhance temperature resistance, which could apply to crops. Furthermore, such insights may also help to preserve wild plant species facing climate-driven extinction risks (Nievola <i>et al</i>., <span>2017</span>). <blockquote><p><i>By integrating thermal proteomics experimental data with a machine learning algorithm, this hybrid parameter estimation strategy resolves a critical limitation in the development of large-scale models</i>…</p>\u0000<div></div>\u0000</blockquote>\u0000</div>\u0000<p>Plants have a limited capacity to regulate their canopy temperature (Guo <i>et al</i>., <span>2023</span>), which means that all internal metabolic reactions are influenced by external temperature fluctuations. Research on signaling transduction, epigenetic regulation, transcriptional networks, and post-translational regulation of heat and cold stress has gained significant attention (Ohama <i>et al</i>., <span>2017</span>; Ding & Yang, <span>2022</span>). However, responses to temperature changes in plants are initially observed at the metabolic level, with subsequent changes in gene expression to restore homeostasis (Casal & Balasubramanian, <span>2019</span>).</p>\u0000<p>Predicting how temperature fluctuations affect overall plant metabolism remains a challenge because the direct temperature effects on individual metabolic enzymes are often not well defined quantitatively. To overcome this challenge, the authors have developed the <i>ecAraCore</i> model, which is an enzyme-constrained extension of the AraCore model (Arnold & Nikoloski, <span>2014</span>). The ","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"14 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Antoine Van de Vloet, Lucas Prost-Boxoen, Quinten Bafort, Yunn Thet Paing, Griet Casteleyn, Lucile Jomat, Stéphane D. Lemaire, Olivier De Clerck, Yves Van de Peer
Whole-genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. Chlamydomonas reinhardtii is a valuable model organism with profound potential to study the impact of ploidy increase on the longer term in a laboratory environment. This is partly due to the ability to increase the ploidy level.
We developed a strategy to engineer ploidy in C. reinhardtii using noninterfering, antibiotic, selectable markers. This approach allows us to induce higher ploidy levels in C. reinhardtii and is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy.
We demonstrate the creation of diploids, triploids, and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles in C. reinhardtii. However, our newly formed triploids and tetraploids show signs of rapid aneuploidization.
Our study greatly facilitates the application of C. reinhardtii to study polyploidy, in both fundamental and applied settings.
{"title":"Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii","authors":"Antoine Van de Vloet, Lucas Prost-Boxoen, Quinten Bafort, Yunn Thet Paing, Griet Casteleyn, Lucile Jomat, Stéphane D. Lemaire, Olivier De Clerck, Yves Van de Peer","doi":"10.1111/nph.70095","DOIUrl":"10.1111/nph.70095","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 </p><ul>\u0000 \u0000 <li>Whole-genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. <i>Chlamydomonas reinhardtii</i> is a valuable model organism with profound potential to study the impact of ploidy increase on the longer term in a laboratory environment. This is partly due to the ability to increase the ploidy level.</li>\u0000 \u0000 <li>We developed a strategy to engineer ploidy in <i>C. reinhardtii</i> using noninterfering, antibiotic, selectable markers. This approach allows us to induce higher ploidy levels in <i>C. reinhardtii</i> and is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy.</li>\u0000 \u0000 <li>We demonstrate the creation of diploids, triploids, and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles in <i>C. reinhardtii</i>. However, our newly formed triploids and tetraploids show signs of rapid aneuploidization.</li>\u0000 \u0000 <li>Our study greatly facilitates the application of <i>C. reinhardtii</i> to study polyploidy, in both fundamental and applied settings.</li>\u0000 </ul>\u0000 </div>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"246 3","pages":"1403-1412"},"PeriodicalIF":8.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Clara Blonde, Amélie Caddeo, William Nasser, Sylvie Reverchon, Rémi Peyraud, Feth el Zahar Haichar
Plant disease outbreaks, exacerbated by climate change, threaten food security and environmental sustainability world-wide. Plants interact with a wide range of microorganisms. The quest for resilient agriculture requires a deep insight into the molecular and ecological interplays between plants and their associated microbial communities. Omics methods, by profiling entire molecular sets, have shed light on these complex interactions. Nonetheless, deciphering the relationships among thousands of molecular components remains a formidable challenge, and studies that integrate these components into cohesive biological networks involving plants and associated microbes are still limited. Systems biology has the potential to predict the effects of biotic and abiotic perturbations on these networks. It is therefore a promising framework for addressing the full complexity of plant–microbiome interactions.
{"title":"New insights in metabolism modelling to decipher plant–microbe interactions","authors":"Clara Blonde, Amélie Caddeo, William Nasser, Sylvie Reverchon, Rémi Peyraud, Feth el Zahar Haichar","doi":"10.1111/nph.70063","DOIUrl":"https://doi.org/10.1111/nph.70063","url":null,"abstract":"Plant disease outbreaks, exacerbated by climate change, threaten food security and environmental sustainability world-wide. Plants interact with a wide range of microorganisms. The quest for resilient agriculture requires a deep insight into the molecular and ecological interplays between plants and their associated microbial communities. Omics methods, by profiling entire molecular sets, have shed light on these complex interactions. Nonetheless, deciphering the relationships among thousands of molecular components remains a formidable challenge, and studies that integrate these components into cohesive biological networks involving plants and associated microbes are still limited. Systems biology has the potential to predict the effects of biotic and abiotic perturbations on these networks. It is therefore a promising framework for addressing the full complexity of plant–microbiome interactions.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"3 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wanpeng Xiang, Ye Jin, Yizhong Wang, Shiming Han, Lei He, Ye Fan, Jing Zhou, Huazhong Shi, Wannian Yang
U2AF65B is one of the splicing factors that are involved in the recognition of the 3′ splicing site and it plays an important role in plant development and stress response through its mRNA splicing function. However, it is not clear whether U2AF65B regulates gene expression in a splicing-independent manner.
Through mutant screening and map-based cloning, protein–protein interaction, transcriptomic sequencing, whole-genome bisulfite sequencing and chromatin immunoprecipitation analysis, we investigated the function of U2AF65B in gene silencing in Arabidopsis thaliana.
We found in the u2af65b mutant that the exogenous transgene 35S::HYG is activated in expression with decreased DNA methylation on the 35S core-promoter compared with that in the wild-type. Loss of U2AF65B function also globally decreased the methylation of CG, CHG and CHH with a profound effect on CHH methylation in transposons and intergenic sequences. Among the hypomethylated non-CG cytosines in u2af65b, nearly half of them are also hypomethylated in the dms3 mutant. Interestingly, U2AF65B interacts with the RNA-directed DNA methylation (RdDM) pathway component DMS3, and loss of U2AF65B function significantly decreased the enrichment of DMS3 on the targets, including the 35S::HYG transgene and endogenous RdDM loci.
Our findings suggest that U2AF65B is a crucial player in RdDM-mediated DNA methylation, partially through promoting the RdDM pathway by interacting with and recruiting DMS3 to the target sequences.
{"title":"The splicing factor U2AF65B regulates cytosine methylation through interacting with DEFECTIVE IN MERISTEM SILENCING 3 in Arabidopsis","authors":"Wanpeng Xiang, Ye Jin, Yizhong Wang, Shiming Han, Lei He, Ye Fan, Jing Zhou, Huazhong Shi, Wannian Yang","doi":"10.1111/nph.70078","DOIUrl":"https://doi.org/10.1111/nph.70078","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>U2AF65B is one of the splicing factors that are involved in the recognition of the 3′ splicing site and it plays an important role in plant development and stress response through its mRNA splicing function. However, it is not clear whether U2AF65B regulates gene expression in a splicing-independent manner.</li>\u0000<li>Through mutant screening and map-based cloning, protein–protein interaction, transcriptomic sequencing, whole-genome bisulfite sequencing and chromatin immunoprecipitation analysis, we investigated the function of U2AF65B in gene silencing in <i>Arabidopsis thaliana</i>.</li>\u0000<li>We found in the <i>u2af65b</i> mutant that the exogenous transgene <i>35S::HYG</i> is activated in expression with decreased DNA methylation on the <i>35S</i> core-promoter compared with that in the wild-type. Loss of U2AF65B function also globally decreased the methylation of CG, CHG and CHH with a profound effect on CHH methylation in transposons and intergenic sequences. Among the hypomethylated non-CG cytosines in <i>u2af65b</i>, nearly half of them are also hypomethylated in the <i>dms3</i> mutant. Interestingly, U2AF65B interacts with the RNA-directed DNA methylation (RdDM) pathway component DMS3, and loss of U2AF65B function significantly decreased the enrichment of DMS3 on the targets, including the <i>35S::HYG</i> transgene and endogenous RdDM loci.</li>\u0000<li>Our findings suggest that U2AF65B is a crucial player in RdDM-mediated DNA methylation, partially through promoting the RdDM pathway by interacting with and recruiting DMS3 to the target sequences.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"33 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
My early years were spent in Kokoda in Papua New Guinea (where my dad was a teacher) – a place where one lived surrounded by forests and grasslands. From family albums, it is clear that we spent a lot of time playing barefoot outdoors, surrounded by, and immersed in lush tropical vegetation. On returning to Australia as a 6-year-old, I had to adjust to wearing shoes in an ordered, suburban landscape that lacked Kokoda's greenness. A yearning for green-dominated environments played a role in my interest in plants, along with: talking to my grandfather about what he was growing in his vegetable garden (and debating whether he really needed to chop down a tree that was shading his vegetables !); and, an uncle introducing me to the landscape wonders of bushwalking and back country cross-country skiing in Australia's high country. These experiences gave me a deep emotional appreciation for the role plants play in regulating ecosystem services and in defining the ‘human condition’. Then, in time, I became fascinated with the question of how plants survive where they do and what factors regulate their ability to grow and reproduce.
{"title":"Owen Atkin","authors":"","doi":"10.1111/nph.70097","DOIUrl":"https://doi.org/10.1111/nph.70097","url":null,"abstract":"<h2> What inspired your interest in plant science?</h2>\u0000<p>My early years were spent in Kokoda in Papua New Guinea (where my dad was a teacher) – a place where one lived surrounded by forests and grasslands. From family albums, it is clear that we spent a lot of time playing barefoot outdoors, surrounded by, and immersed in lush tropical vegetation. On returning to Australia as a 6-year-old, I had to adjust to wearing shoes in an ordered, suburban landscape that lacked Kokoda's greenness. A yearning for green-dominated environments played a role in my interest in plants, along with: talking to my grandfather about what he was growing in his vegetable garden (and debating whether he really needed to chop down a tree that was shading his vegetables !); and, an uncle introducing me to the landscape wonders of bushwalking and back country cross-country skiing in Australia's high country. These experiences gave me a deep emotional appreciation for the role plants play in regulating ecosystem services and in defining the ‘human condition’. Then, in time, I became fascinated with the question of how plants survive where they do and what factors regulate their ability to grow and reproduce.</p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"183 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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