Anju Manandhar, Ian M. Rimer, Talitha Soares Pereira, Javier Pichaco, Fulton E. Rockwell, Scott A. M. McAdam
气孔开始关闭会减少干旱期间的蒸腾作用。在种子植物中，干旱会导致植物水分状况下降，从而增加气孔关闭所需的叶片内源脱落酸（ABA）水平。在土壤-植物大气连续体中有多个可能的地下阻力增加点，这些阻力点会使叶片水势下降到足以引发 ABA 生成和随后蒸腾作用下降的程度。我们利用干旱期间对叶片水势的连续树枝仪测量，研究了高抗栓塞物种 Callitris tuberculata 的叶片 ABA 水平、植物水力传导以及土壤-植物传导失效点的动态模式。我们发现，在黎明前水势永久性下降、土壤-植物水力通路崩溃和木质部栓塞蔓延之前，蒸腾作用和 ABA 生物合成就已经开始下降。我们发现，ABA 生物合成所需的正午叶片水势下降和蒸腾作用开始下降的最可能驱动因素是靠近根部的土壤中动态但可恢复的水力阻力增加。
{"title":"Dynamic soil hydraulic resistance regulates stomata","authors":"Anju Manandhar, Ian M. Rimer, Talitha Soares Pereira, Javier Pichaco, Fulton E. Rockwell, Scott A. M. McAdam","doi":"10.1111/nph.20020","DOIUrl":"10.1111/nph.20020","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.20020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chloroplasts play a crucial role in plant defense against pathogens, making them primary targets for pathogen effectors that suppress host immunity. This study characterizes the Plasmopara viticola CRN-like effector, PvCRN20, which interacts with DEG5 in the cytoplasm but not with its interacting protein, DEG8, which is located in the chloroplast.
By transiently overexpressing in tobacco leaves, we show that PvCRN20 could inhibit INF1- and Bax-triggered cell death. Constitutive expression of PvCRN20 suppresses the accumulation of reactive oxygen species (ROS) and promotes pathogen colonization. PvCRN20 reduces DEG5 entry into chloroplasts, thereby disrupting DEG5 and DEG8 interactions in chloroplasts.
Overexpression of VvDEG5 and VvDEG8 induces ROS accumulation and enhances grapevine resistance to P. viticola, whereas knockout of VvDEG8 represses ROS production and promotes P. viticola colonization. Consistently, ectopic expression of VvDEG5 and VvDEG8 in tobacco promotes chloroplast-derived ROS accumulation, whereas co-expression of PvCRN20 counteracted this promotion by VvDEG5. Therefore, DEG5 is essential for the virulence function of PvCRN20. Although PvCRN20 is located in both the nucleus and cytoplasm, only cytoplasmic PvCRN20 suppresses plant immunity and promotes pathogen infection.
Our results reveal that PvCRN20 dampens plant defenses by repressing the chloroplast import of DEG5, thus reducing host ROS accumulation and facilitating pathogen colonization.
{"title":"Plasmopara viticola effector PvCRN20 represses the import of VvDEG5 into chloroplasts to suppress immunity in grapevine","authors":"Qingqing Fu, Tingting Chen, Yunlei Wang, Huixuan Zhou, Kangzhuang Zhang, Runlong Zheng, Yanan Zhang, Ruiqi Liu, Xiao Yin, Guotian Liu, Yan Xu","doi":"10.1111/nph.20002","DOIUrl":"10.1111/nph.20002","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 \u0000 </p><ul>\u0000 \u0000 \u0000 <li>Chloroplasts play a crucial role in plant defense against pathogens, making them primary targets for pathogen effectors that suppress host immunity. This study characterizes the <i>Plasmopara viticola</i> CRN-like effector, PvCRN20, which interacts with DEG5 in the cytoplasm but not with its interacting protein, DEG8, which is located in the chloroplast.</li>\u0000 \u0000 \u0000 <li>By transiently overexpressing in tobacco leaves, we show that PvCRN20 could inhibit INF1- and Bax-triggered cell death. Constitutive expression of PvCRN20 suppresses the accumulation of reactive oxygen species (ROS) and promotes pathogen colonization. PvCRN20 reduces DEG5 entry into chloroplasts, thereby disrupting DEG5 and DEG8 interactions in chloroplasts.</li>\u0000 \u0000 \u0000 <li>Overexpression of VvDEG5 and VvDEG8 induces ROS accumulation and enhances grapevine resistance to <i>P. viticola</i>, whereas knockout of VvDEG8 represses ROS production and promotes <i>P. viticola</i> colonization. Consistently, ectopic expression of VvDEG5 and VvDEG8 in tobacco promotes chloroplast-derived ROS accumulation, whereas co-expression of PvCRN20 counteracted this promotion by VvDEG5. Therefore, DEG5 is essential for the virulence function of PvCRN20. Although PvCRN20 is located in both the nucleus and cytoplasm, only cytoplasmic PvCRN20 suppresses plant immunity and promotes pathogen infection.</li>\u0000 \u0000 \u0000 <li>Our results reveal that PvCRN20 dampens plant defenses by repressing the chloroplast import of DEG5, thus reducing host ROS accumulation and facilitating pathogen colonization.</li>\u0000 </ul>\u0000 \u0000 </div>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876442","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}
<p>The anther is a critical male organ for plant reproduction in flowering plants. In rice (<i>Oryza sativa</i> L.), anthers consist of four somatic cell layers named epidermis, endothecium, middle layer and tapetum, which surround the reproductive cells (Zhang <i>et al</i>., <span>2011</span>). The rice anther is of particular interest for crop breeding researchers because the male sterile line, mostly resulting from anther developmental defect, is the core component for hybrid rice breeding. Ubisch bodies, the unique U-shaped secretory structures distributed in the inner surface of tapetum, mediate exporting tapetum-produced sugars, lipids, proteins and sporopollenin precursors to facilitate microspore development. Reactive oxygen species (ROS), including H<sub>2</sub>O<sub>2</sub> and superoxide anion (O<sub>2</sub><sup>•−</sup>) as important oxidizing agents in living cells, have been reported to trigger tapetal programmed cell death (PCD) and thus male sterility in rice (Hu <i>et al</i>., <span>2011</span>; Luo <i>et al</i>., <span>2013</span>). However, the regulation of ROS homeostasis in tapetum development, Ubisch body formation and its impact on male fertility remain unclear.</p><p>To gain insight into the genetic regulation of male sterility in rice, we identified a mutant named <i>no ubisch body and pollen grain 1</i> (<i>nup1</i>) from a tissue culture-induced mutant library in the <i>indica</i> cv MingHui86 (MH86). At maturity, the <i>nup1</i> mutant exhibited a slightly enclosed panicle, and smaller and paler yellow anthers with no pollen grain and seed production compared with the wild-type (WT) MH86, while plant architecture, female organ and spikelet showed no obvious differences (Fig. 1a–e, Supporting Information Fig. S1), indicating that the <i>nup1</i> mutant is male sterility. Upon pollination of the <i>nup1</i> mutant with the pollen grains of WT, all the F<sub>1</sub> plants exhibited normal fertility and the F<sub>2</sub> plants showed a segregation of 249 fertile and 78 sterile plants (3 : 1, <i>χ</i><sup>2</sup> = 0.26, <i>P</i> > 0.05), demonstrating that this male sterile phenotype is controlled by a single recessive gene. To investigate the cytological defects of the <i>nup1</i> mutant, anthers were analyzed through semi-thin sections based on anther developmental stages as described previously (Zhang <i>et al</i>., <span>2011</span>). We found that no differences were visible between the <i>nup1</i> mutant and WT during Stage 7 (S7) to Stage 9 (S9) (Fig. S2a). Notably, the <i>nup1</i> mutant exhibited obviously shrinking tapetal cells and swollen microspores at S10 and S11, but the swollen microspores rapidly shriveled and crushed at late S11 and S12 (Figs 1f,g, S2b), resulting in no pollen grain production compared with the WT which underwent the regular anther developments.</p><p>Transmission electron microscopy (TEM) analysis was performed as described in Methods S1 to observe more detailed structure changes i
{"title":"Oxidative burst causes loss of tapetal Ubisch body and male sterility in rice","authors":"Chuanlin Shi, Shaohua Yang, Yan Cui, Zhan Xu, Bin Zhang, Mingliang Guo, Yiwang Zhu, Ying Yang, Feng Wang, Huaqing Liu, Yu Zhang, Qian Qian, Lianguang Shang","doi":"10.1111/nph.20023","DOIUrl":"10.1111/nph.20023","url":null,"abstract":"<p>The anther is a critical male organ for plant reproduction in flowering plants. In rice (<i>Oryza sativa</i> L.), anthers consist of four somatic cell layers named epidermis, endothecium, middle layer and tapetum, which surround the reproductive cells (Zhang <i>et al</i>., <span>2011</span>). The rice anther is of particular interest for crop breeding researchers because the male sterile line, mostly resulting from anther developmental defect, is the core component for hybrid rice breeding. Ubisch bodies, the unique U-shaped secretory structures distributed in the inner surface of tapetum, mediate exporting tapetum-produced sugars, lipids, proteins and sporopollenin precursors to facilitate microspore development. Reactive oxygen species (ROS), including H<sub>2</sub>O<sub>2</sub> and superoxide anion (O<sub>2</sub><sup>•−</sup>) as important oxidizing agents in living cells, have been reported to trigger tapetal programmed cell death (PCD) and thus male sterility in rice (Hu <i>et al</i>., <span>2011</span>; Luo <i>et al</i>., <span>2013</span>). However, the regulation of ROS homeostasis in tapetum development, Ubisch body formation and its impact on male fertility remain unclear.</p><p>To gain insight into the genetic regulation of male sterility in rice, we identified a mutant named <i>no ubisch body and pollen grain 1</i> (<i>nup1</i>) from a tissue culture-induced mutant library in the <i>indica</i> cv MingHui86 (MH86). At maturity, the <i>nup1</i> mutant exhibited a slightly enclosed panicle, and smaller and paler yellow anthers with no pollen grain and seed production compared with the wild-type (WT) MH86, while plant architecture, female organ and spikelet showed no obvious differences (Fig. 1a–e, Supporting Information Fig. S1), indicating that the <i>nup1</i> mutant is male sterility. Upon pollination of the <i>nup1</i> mutant with the pollen grains of WT, all the F<sub>1</sub> plants exhibited normal fertility and the F<sub>2</sub> plants showed a segregation of 249 fertile and 78 sterile plants (3 : 1, <i>χ</i><sup>2</sup> = 0.26, <i>P</i> > 0.05), demonstrating that this male sterile phenotype is controlled by a single recessive gene. To investigate the cytological defects of the <i>nup1</i> mutant, anthers were analyzed through semi-thin sections based on anther developmental stages as described previously (Zhang <i>et al</i>., <span>2011</span>). We found that no differences were visible between the <i>nup1</i> mutant and WT during Stage 7 (S7) to Stage 9 (S9) (Fig. S2a). Notably, the <i>nup1</i> mutant exhibited obviously shrinking tapetal cells and swollen microspores at S10 and S11, but the swollen microspores rapidly shriveled and crushed at late S11 and S12 (Figs 1f,g, S2b), resulting in no pollen grain production compared with the WT which underwent the regular anther developments.</p><p>Transmission electron microscopy (TEM) analysis was performed as described in Methods S1 to observe more detailed structure changes i","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.20023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Secondary cell walls (SCWs) of tracheary elements emerged in the Silurian some 430 million years ago (Ma) and were essential to the evolutionary success of plants after land colonization (Edwards, 2003; Gerrienne et al., 2011; Edwards & Kenrick, 2015; Pfeiler & Tomescu, 2023). They are the key feature of woody plants, providing structural support for upwards growth and resisting the negative pressure from water transport in the xylem. SCWs are laid down after the formation of the primary cell wall (PCW). While PCWs are, by design, generally thin, extensible and subject to remodelling to permit cell growth, SCWs provide reinforcement and the bulk of woody biomass (Ramage et al., 2017). The SCWs are therefore central to plant physiology, yet our knowledge of their evolution and structural diversity in the plant kingdom is limited and impairs our understanding of the structure-to-function relationship for this important cellular component. Moreover, since SCWs are the largest repository of carbon in the biosphere (Bar-On et al., 2018), a better understanding of their diversity may further our attempts to mitigate the climate emergency through, for example, evidence-based design of reforestation policies.
Secondary cell wall is a matrix composed of polysaccharides, principally cellulose and hemicelluloses, impregnated with a polyphenolic hydrophobic compound known as lignin. The beta-1,4-linked glucose chains coallesce into the cellulose microfibril, which is 3–4 nm in size, with several microfibrils plus other cell wall components forming the macrofibril – a cylindrical structure with a diameter of between 10 and 40 nm (Donaldson, 2007; Lyczakowski et al., 2019). The interaction between the cell wall components occurring within the cell wall macrofibril may be central to the SCW properties such as mechanical strength, recalcitrance to enzymatic degradation or water transport capacity (Grantham et al., 2017; Lyczakowski et al., 2017; Terrett & Dupree, 2019; Cresswell et al., 2021).
Our previous analysis (Lyczakowski et al., 2019) used low-temperature scanning electron microscopy, known as cryoSEM, for high-magnification imaging to resolve individual macrofibrils in live, hydrated wood samples. We demonstrated that cell wall macrofibrils are smaller in the model angiosperm tree species, Populus tremula × tremuloides, than they are in the model gymnosperm tree, Picea abies. This may be associated with differences in cell wall composition and may reflect variation in interactions within the cell wall matrix, which in turn may influence wood properties. Therefore, the exact structure of macrofibrils may be important in determining qualities such as wood porosity, strength or its capacity to st
{"title":"Convergent and adaptive evolution drove change of secondary cell wall ultrastructure in extant lineages of seed plants","authors":"Jan J. Lyczakowski, Raymond Wightman","doi":"10.1111/nph.19983","DOIUrl":"10.1111/nph.19983","url":null,"abstract":"<p>Secondary cell walls (SCWs) of tracheary elements emerged in the Silurian some 430 million years ago (Ma) and were essential to the evolutionary success of plants after land colonization (Edwards, <span>2003</span>; Gerrienne <i>et al</i>., <span>2011</span>; Edwards & Kenrick, <span>2015</span>; Pfeiler & Tomescu, <span>2023</span>). They are the key feature of woody plants, providing structural support for upwards growth and resisting the negative pressure from water transport in the xylem. SCWs are laid down after the formation of the primary cell wall (PCW). While PCWs are, by design, generally thin, extensible and subject to remodelling to permit cell growth, SCWs provide reinforcement and the bulk of woody biomass (Ramage <i>et al</i>., <span>2017</span>). The SCWs are therefore central to plant physiology, yet our knowledge of their evolution and structural diversity in the plant kingdom is limited and impairs our understanding of the structure-to-function relationship for this important cellular component. Moreover, since SCWs are the largest repository of carbon in the biosphere (Bar-On <i>et al</i>., <span>2018</span>), a better understanding of their diversity may further our attempts to mitigate the climate emergency through, for example, evidence-based design of reforestation policies.</p><p>Secondary cell wall is a matrix composed of polysaccharides, principally cellulose and hemicelluloses, impregnated with a polyphenolic hydrophobic compound known as lignin. The beta-1,4-linked glucose chains coallesce into the cellulose microfibril, which is 3–4 nm in size, with several microfibrils plus other cell wall components forming the macrofibril – a cylindrical structure with a diameter of between 10 and 40 nm (Donaldson, <span>2007</span>; Lyczakowski <i>et al</i>., <span>2019</span>). The interaction between the cell wall components occurring within the cell wall macrofibril may be central to the SCW properties such as mechanical strength, recalcitrance to enzymatic degradation or water transport capacity (Grantham <i>et al</i>., <span>2017</span>; Lyczakowski <i>et al</i>., <span>2017</span>; Terrett & Dupree, <span>2019</span>; Cresswell <i>et al</i>., <span>2021</span>).</p><p>Our previous analysis (Lyczakowski <i>et al</i>., <span>2019</span>) used low-temperature scanning electron microscopy, known as cryoSEM, for high-magnification imaging to resolve individual macrofibrils in live, hydrated wood samples. We demonstrated that cell wall macrofibrils are smaller in the model angiosperm tree species, <i>Populus tremula × tremuloides</i>, than they are in the model gymnosperm tree, <i>Picea abies</i>. This may be associated with differences in cell wall composition and may reflect variation in interactions within the cell wall matrix, which in turn may influence wood properties. Therefore, the exact structure of macrofibrils may be important in determining qualities such as wood porosity, strength or its capacity to st","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19983","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hanna Eriksdotter Thosteman, Katherine Eisen, Hampus Petrén, Sotiria Boutsi, Loretta Pace, John M. Halley, Consuelo M. De Moraes, Mark C. Mescher, James Buckley, Magne Friberg
{"title":"Integration of attractive and defensive phytochemicals is unlikely to constrain chemical diversification in a perennial herb","authors":"Hanna Eriksdotter Thosteman, Katherine Eisen, Hampus Petrén, Sotiria Boutsi, Loretta Pace, John M. Halley, Consuelo M. De Moraes, Mark C. Mescher, James Buckley, Magne Friberg","doi":"10.1111/nph.20006","DOIUrl":"10.1111/nph.20006","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.20006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marybel Soto Gomez, Matilda J. M. Brown, Samuel Pironon, Petr Bureš, Luis D. Verde Arregoitia, Pavel Veselý, Tammy L. Elliott, František Zedek, Jaume Pellicer, Félix Forest, Eimear Nic Lughadha, Ilia J. Leitch
{"title":"Genome size is positively correlated with extinction risk in herbaceous angiosperms","authors":"Marybel Soto Gomez, Matilda J. M. Brown, Samuel Pironon, Petr Bureš, Luis D. Verde Arregoitia, Pavel Veselý, Tammy L. Elliott, František Zedek, Jaume Pellicer, Félix Forest, Eimear Nic Lughadha, Ilia J. Leitch","doi":"10.1111/nph.19947","DOIUrl":"10.1111/nph.19947","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19947","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Taein Kim, Seul Lee, Yejin Kwak, Min-Soo Choi, Jeongbin Park, Sung Ju Hwang, Sang-Gyu Kim
Plants, as a sessile organism, produce various secondary metabolites to interact with the environment. These chemicals have fascinated the plant science community because of their ecological significance and notable biological activity. However, predicting the complete biosynthetic pathways from target molecules to metabolic building blocks remains a challenge.
Here, we propose retrieval-augmented dual-view retrosynthesis (READRetro) as a practical bio-retrosynthesis tool to predict the biosynthetic pathways of plant natural products. Conventional bio-retrosynthesis models have been limited in their ability to predict biosynthetic pathways for natural products. READRetro was optimized for the prediction of complex metabolic pathways by incorporating cutting-edge deep learning architectures, an ensemble approach, and two retrievers.
Evaluation of single- and multi-step retrosynthesis showed that each component of READRetro significantly improved its ability to predict biosynthetic pathways. READRetro was also able to propose the known pathways of secondary metabolites such as monoterpene indole alkaloids and the unknown pathway of menisdaurilide, demonstrating its applicability to real-world bio-retrosynthesis of plant natural products.
For researchers interested in the biosynthesis and production of secondary metabolites, a user-friendly website (https://readretro.net) and the open-source code of READRetro have been made available.
{"title":"READRetro: natural product biosynthesis predicting with retrieval-augmented dual-view retrosynthesis","authors":"Taein Kim, Seul Lee, Yejin Kwak, Min-Soo Choi, Jeongbin Park, Sung Ju Hwang, Sang-Gyu Kim","doi":"10.1111/nph.20012","DOIUrl":"10.1111/nph.20012","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 \u0000 </p><ul>\u0000 \u0000 \u0000 <li>Plants, as a sessile organism, produce various secondary metabolites to interact with the environment. These chemicals have fascinated the plant science community because of their ecological significance and notable biological activity. However, predicting the complete biosynthetic pathways from target molecules to metabolic building blocks remains a challenge.</li>\u0000 \u0000 \u0000 <li>Here, we propose retrieval-augmented dual-view retrosynthesis (READRetro) as a practical bio-retrosynthesis tool to predict the biosynthetic pathways of plant natural products. Conventional bio-retrosynthesis models have been limited in their ability to predict biosynthetic pathways for natural products. READRetro was optimized for the prediction of complex metabolic pathways by incorporating cutting-edge deep learning architectures, an ensemble approach, and two retrievers.</li>\u0000 \u0000 \u0000 <li>Evaluation of single- and multi-step retrosynthesis showed that each component of READRetro significantly improved its ability to predict biosynthetic pathways. READRetro was also able to propose the known pathways of secondary metabolites such as monoterpene indole alkaloids and the unknown pathway of menisdaurilide, demonstrating its applicability to real-world bio-retrosynthesis of plant natural products.</li>\u0000 \u0000 \u0000 <li>For researchers interested in the biosynthesis and production of secondary metabolites, a user-friendly website (https://readretro.net) and the open-source code of READRetro have been made available.</li>\u0000 </ul>\u0000 \u0000 </div>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856856","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}
Ryuta Yagi, Takashi F. Haraguchi, Ichiro Tayasu, Kenji Suetsugu
To evaluate the nutritional modes of orchids associated with ‘rhizoctonia’ fungi, analyses of hydrogen (δ2H), carbon (δ13C), and nitrogen (δ15N) stable isotope ratios are usually adopted. However, previous studies have not fully accounted for exchangeable hydrogens, which could affect these evaluations.
Here, we performed standard δ13C, δ15N, and δ2H analyses on bulk samples. Additionally, we conducted δ2H analysis on α-cellulose and cellulose nitrate samples to investigate whether the heterogeneity of exchangeable hydrogens among plant species influences the assessment of nutritional modes.
The δ2H of orchids were consistently higher than those of surrounding autotrophic plants, irrespective of the three pretreatments. Although the rhizoctonia-associated orchid exhibited lower δ13C, its δ2H was higher than those of the autotrophs. Notably, among all response variables, δ15N and δ2H exhibited high abilities for discriminating the nutritional modes of rhizoctonia-associated orchids.
These results indicate that a time-efficient bulk sample analysis is an effective method for evaluating plant nutritional modes, as the heterogeneity of exchangeable hydrogens does not significantly impact the estimation. Using δ15N and δ2H benefits the assessment of partial mycoheterotrophy among rhizoctonia-associated orchids.
{"title":"Do exchangeable hydrogens affect the evaluation of partial mycoheterotrophy in orchids? Insights from δ2H analysis in bulk, α-cellulose, and cellulose nitrate samples","authors":"Ryuta Yagi, Takashi F. Haraguchi, Ichiro Tayasu, Kenji Suetsugu","doi":"10.1111/nph.19998","DOIUrl":"10.1111/nph.19998","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 \u0000 </p><ul>\u0000 \u0000 \u0000 <li>To evaluate the nutritional modes of orchids associated with ‘rhizoctonia’ fungi, analyses of hydrogen (δ<sup>2</sup>H), carbon (δ<sup>13</sup>C), and nitrogen (δ<sup>15</sup>N) stable isotope ratios are usually adopted. However, previous studies have not fully accounted for exchangeable hydrogens, which could affect these evaluations.</li>\u0000 \u0000 \u0000 <li>Here, we performed standard δ<sup>13</sup>C, δ<sup>15</sup>N, and δ<sup>2</sup>H analyses on bulk samples. Additionally, we conducted δ<sup>2</sup>H analysis on α-cellulose and cellulose nitrate samples to investigate whether the heterogeneity of exchangeable hydrogens among plant species influences the assessment of nutritional modes.</li>\u0000 \u0000 \u0000 <li>The δ<sup>2</sup>H of orchids were consistently higher than those of surrounding autotrophic plants, irrespective of the three pretreatments. Although the rhizoctonia-associated orchid exhibited lower δ<sup>13</sup>C, its δ<sup>2</sup>H was higher than those of the autotrophs. Notably, among all response variables, δ<sup>15</sup>N and δ<sup>2</sup>H exhibited high abilities for discriminating the nutritional modes of rhizoctonia-associated orchids.</li>\u0000 \u0000 \u0000 <li>These results indicate that a time-efficient bulk sample analysis is an effective method for evaluating plant nutritional modes, as the heterogeneity of exchangeable hydrogens does not significantly impact the estimation. Using δ<sup>15</sup>N and δ<sup>2</sup>H benefits the assessment of partial mycoheterotrophy among rhizoctonia-associated orchids.</li>\u0000 </ul>\u0000 \u0000 </div>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856853","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}
Chemical-inducible gene expression systems are commonly used to regulate gene expression for functional genomics in various plant species. However, a convenient system that can tightly regulate transgene expression in Nicotiana benthamiana is still lacking.
In this study, we developed a tightly regulated copper-inducible system that can control transgene expression and conduct cell death assays in N. benthamiana. We tested several chemical-inducible systems using Agrobacterium-mediated transient expression and found that the copper-inducible system exhibited the least concerns regarding leakiness in N. benthamiana. Although the copper-inducible system can control the expression of some tested reporters, it is not sufficiently tight to regulate certain tested hypersensitive cell death responses. Using the MoClo-based synthetic biology approach, we incorporated the suicide exon HyP5SM/OsL5 and Cre/LoxP as additional regulatory elements to enhance the tightness of the regulation.
This new design allowed us to tightly control the hypersensitive cell death induced by several tested leucine-rich repeat-containing proteins and their matching avirulence factors, and it can be easily applied to regulate the expression of other transgenes in transient expression assays.
Our findings offer new approaches for both fundamental and translational studies in plant functional genomics.
化学诱导基因表达系统常用于调控各种植物物种的功能基因组学基因表达。然而，目前仍缺乏一种可严格调控转基因表达的简便系统。在本研究中，我们开发了一种能严格调控铜诱导系统，该系统能控制转基因的表达，并能在 N. benthamiana 中进行细胞死亡检测。我们利用农杆菌介导的瞬时表达测试了几种化学诱导系统，发现铜诱导系统在 N. benthamiana 中的泄漏问题最小。虽然铜诱导系统可以控制一些测试报告的表达，但它在调控某些测试的超敏细胞死亡反应方面不够严密。利用基于 MoClo 的合成生物学方法，我们加入了自杀外显子 HyP5SM/OsL5 和 Cre/LoxP 作为额外的调控元件，以提高调控的严密性。这种新设计使我们能够严格控制几种经测试的含富含亮氨酸重复蛋白及其匹配的无毒因子所诱导的超敏细胞死亡，而且它还可以很容易地应用于瞬时表达试验中其他转基因的表达调控。我们的发现为植物功能基因组学的基础研究和转化研究提供了新方法。
{"title":"Development of a tightly regulated copper-inducible transient gene expression system in Nicotiana benthamiana incorporating a suicide exon and Cre recombinase","authors":"Bing-Jen Chiang, Kuan-Yu Lin, Yi-Feng Chen, Ching-Yi Huang, Foong-Jing Goh, Lo-Ting Huang, Li-Hung Chen, Chih-Hang Wu","doi":"10.1111/nph.20021","DOIUrl":"10.1111/nph.20021","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 \u0000 </p><ul>\u0000 \u0000 \u0000 <li>Chemical-inducible gene expression systems are commonly used to regulate gene expression for functional genomics in various plant species. However, a convenient system that can tightly regulate transgene expression in <i>Nicotiana benthamiana</i> is still lacking.</li>\u0000 \u0000 \u0000 <li>In this study, we developed a tightly regulated copper-inducible system that can control transgene expression and conduct cell death assays in <i>N. benthamiana</i>. We tested several chemical-inducible systems using <i>Agrobacterium</i>-mediated transient expression and found that the copper-inducible system exhibited the least concerns regarding leakiness in <i>N. benthamiana.</i> Although the copper-inducible system can control the expression of some tested reporters, it is not sufficiently tight to regulate certain tested hypersensitive cell death responses. Using the MoClo-based synthetic biology approach, we incorporated the suicide exon <i>HyP5SM</i>/OsL5 and Cre/<i>LoxP</i> as additional regulatory elements to enhance the tightness of the regulation.</li>\u0000 \u0000 \u0000 <li>This new design allowed us to tightly control the hypersensitive cell death induced by several tested leucine-rich repeat-containing proteins and their matching avirulence factors, and it can be easily applied to regulate the expression of other transgenes in transient expression assays.</li>\u0000 \u0000 \u0000 <li>Our findings offer new approaches for both fundamental and translational studies in plant functional genomics.</li>\u0000 </ul>\u0000 \u0000 </div>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":8.3,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856852","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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