Sarah Philipps, Tobias Pfennig, Elouën Corvest, Marvin van Aalst, Lisa Fürtauer, Anna Matuszyńska
Studies show the advantage of active versus passive learning formats in delivering complicated concepts (Minocha and Clarke, 2009; Pluta et al., 2013). Hence, interactive teaching tools are not only more often positively evaluated by students but also contribute to better life-long teaching outcomes (Ang et al., 2021). Following this evidence, we created ComPhot, a stand-alone learning platform for motivated students and researchers. It guides the user in studying photosynthesis as a well-known biological process with the support of a computational model. ComPhot is a no-code, easy-to-use tool to lower the entry bar for starting the journey across computational biology and to provide insights into how photosynthesis and modeling photosynthesis work. This user-friendly interactive teaching platform can be used individually or to support teachers following a syllabus in biology, to include the concept of computational biology or mathematics, to show the possible field of application of mathematics to biology. ComPhot introduces and explains the biochemical background of our simulated system and how to translate it into mathematical terms. We provide diverse teaching materials that include text, guiding questions, videos, and, most importantly, simulations. Within our simulators, users can perform computational photosynthesis modeling in their browser by simply setting and manipulating slider bars. Our comprehensive approach conveys fundamental insights into photosynthesis, photoprotection, and fluorescence measurements and empowers users to devise their own in silico experiments by varying light conditions or designing synthetic strains. This tool acts as a stepping stone, fostering engagement and understanding while propelling research and innovation in photosynthesis. Although this guide has been written in English, we are proud to release the tool in four of the developers’ languages to expand the audience: English, German, French, and Polish.
{"title":"Computational Photosynthesis (ComPhot): Simulation-Based Learning Platform to Study Photosynthesis","authors":"Sarah Philipps, Tobias Pfennig, Elouën Corvest, Marvin van Aalst, Lisa Fürtauer, Anna Matuszyńska","doi":"10.1093/plcell/koae101","DOIUrl":"https://doi.org/10.1093/plcell/koae101","url":null,"abstract":"Studies show the advantage of active versus passive learning formats in delivering complicated concepts (Minocha and Clarke, 2009; Pluta et al., 2013). Hence, interactive teaching tools are not only more often positively evaluated by students but also contribute to better life-long teaching outcomes (Ang et al., 2021). Following this evidence, we created ComPhot, a stand-alone learning platform for motivated students and researchers. It guides the user in studying photosynthesis as a well-known biological process with the support of a computational model. ComPhot is a no-code, easy-to-use tool to lower the entry bar for starting the journey across computational biology and to provide insights into how photosynthesis and modeling photosynthesis work. This user-friendly interactive teaching platform can be used individually or to support teachers following a syllabus in biology, to include the concept of computational biology or mathematics, to show the possible field of application of mathematics to biology. ComPhot introduces and explains the biochemical background of our simulated system and how to translate it into mathematical terms. We provide diverse teaching materials that include text, guiding questions, videos, and, most importantly, simulations. Within our simulators, users can perform computational photosynthesis modeling in their browser by simply setting and manipulating slider bars. Our comprehensive approach conveys fundamental insights into photosynthesis, photoprotection, and fluorescence measurements and empowers users to devise their own in silico experiments by varying light conditions or designing synthetic strains. This tool acts as a stepping stone, fostering engagement and understanding while propelling research and innovation in photosynthesis. Although this guide has been written in English, we are proud to release the tool in four of the developers’ languages to expand the audience: English, German, French, and Polish.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141185375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Erika Isono, Jianming Li, Pablo Pulido, Wei Siao, Steven H Spoel, Zhishuo Wang, Xiaohong Zhuang, Marco Trujillo
Proteome composition is dynamic and influenced by many internal and external cues, including developmental signals, light availability, or environmental stresses. Protein degradation, in synergy with protein biosynthesis, allows cells to respond to various stimuli and adapt by reshaping the proteome. Protein degradation mediates the final and irreversible disassembly of proteins, which is important for protein quality control and to eliminate misfolded or damaged proteins, as well as entire organelles. Consequently, it contributes to cell resilience by buffering against protein or organellar damage caused by stresses. Moreover, protein degradation plays important roles in cell signaling, as well as transcriptional and translational events. The intricate task of recognizing specific proteins for degradation is achieved by specialized systems that are tailored to the substrate’s physicochemical properties and subcellular localization. These systems recognize diverse substrate cues collectively referred to as “degrons”, which can assume a range of structural configurations. They are molecular surfaces recognized by E3 ligases of the ubiquitin-proteasome system, but can also be considered as general features recognized by other degradation systems, including autophagy or even organellar proteases. Here we provide an overview of the newest developments in the field, delving into the intricate processes of protein recognition and elucidating the pathways through which they are recruited for degradation.
{"title":"Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants","authors":"Erika Isono, Jianming Li, Pablo Pulido, Wei Siao, Steven H Spoel, Zhishuo Wang, Xiaohong Zhuang, Marco Trujillo","doi":"10.1093/plcell/koae141","DOIUrl":"https://doi.org/10.1093/plcell/koae141","url":null,"abstract":"Proteome composition is dynamic and influenced by many internal and external cues, including developmental signals, light availability, or environmental stresses. Protein degradation, in synergy with protein biosynthesis, allows cells to respond to various stimuli and adapt by reshaping the proteome. Protein degradation mediates the final and irreversible disassembly of proteins, which is important for protein quality control and to eliminate misfolded or damaged proteins, as well as entire organelles. Consequently, it contributes to cell resilience by buffering against protein or organellar damage caused by stresses. Moreover, protein degradation plays important roles in cell signaling, as well as transcriptional and translational events. The intricate task of recognizing specific proteins for degradation is achieved by specialized systems that are tailored to the substrate’s physicochemical properties and subcellular localization. These systems recognize diverse substrate cues collectively referred to as “degrons”, which can assume a range of structural configurations. They are molecular surfaces recognized by E3 ligases of the ubiquitin-proteasome system, but can also be considered as general features recognized by other degradation systems, including autophagy or even organellar proteases. Here we provide an overview of the newest developments in the field, delving into the intricate processes of protein recognition and elucidating the pathways through which they are recruited for degradation.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"57 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140821586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Roberta Croce, Elizabete Carmo-Silva, Young B Cho, Maria Ermakova, Jeremy Harbinson, Tracy Lawson, Alistair J McCormick, Krishna K Niyogi, Donald R Ort, Dhruv Patel-Tupper, Paolo Pesaresi, Christine Raines, Andreas P M Weber, Xin-Guang Zhu
Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase CO2 concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.
{"title":"Perspectives on improving photosynthesis to increase crop yield","authors":"Roberta Croce, Elizabete Carmo-Silva, Young B Cho, Maria Ermakova, Jeremy Harbinson, Tracy Lawson, Alistair J McCormick, Krishna K Niyogi, Donald R Ort, Dhruv Patel-Tupper, Paolo Pesaresi, Christine Raines, Andreas P M Weber, Xin-Guang Zhu","doi":"10.1093/plcell/koae132","DOIUrl":"https://doi.org/10.1093/plcell/koae132","url":null,"abstract":"Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase CO2 concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140821578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Grain and flag leaf size are two important agronomic traits that influence grain yield in rice (Oryza sativa). Many QTLs and genes that regulate these traits individually have been identified, however, few QTLs and genes that simultaneously control these two traits have been identified. In this study, we conducted a genome-wide association analysis in rice and detected a major locus, WIDTH OF LEAF AND GRAIN (WLG), that associated with both grain and flag leaf width. WLG encodes a RING-domain E3 ubiquitin ligase. WLGhap.B, which possesses five SNP variations compared to WLGhap.A, encodes a protein with enhanced ubiquitination activity that confers increased rice leaf width and grain size, whereas mutation of WLG leads to narrower leaves and smaller grains. Both WLGhap.A and WLGhap.B interact with LARGE2, a HETC-type E3 ligase, however, WLGhap.B exhibits stronger interaction with LARGE2, thus higher ubiquitination activity towards LARGE2 compared with WLGhap.A. Lysine1021 is crucial for the ubiquitination of LARGE2 by WLG. Loss-of-function of LARGE2 in wlg-1 phenocopies large2-c in grain and leaf width, suggesting that WLG acts upstream of LARGE2. These findings reveal the genetic and molecular mechanism by which the WLG–LARGE2 module mediates grain and leaf size in rice, and suggest the potential of WLGhap.B in improving rice yield.
{"title":"Variation in WIDTH OF LEAF AND GRAIN contributes to grain and leaf size by controlling LARGE2 stability in rice","authors":"Zhichuang Yue, Zhipeng Wang, Yilong Yao, Yuanlin Liang, Jiaying Li, Kaili Yin, Ruiying Li, Yibo Li, Yidan Ouyang, Lizhong Xiong, Honghong Hu","doi":"10.1093/plcell/koae136","DOIUrl":"https://doi.org/10.1093/plcell/koae136","url":null,"abstract":"Grain and flag leaf size are two important agronomic traits that influence grain yield in rice (Oryza sativa). Many QTLs and genes that regulate these traits individually have been identified, however, few QTLs and genes that simultaneously control these two traits have been identified. In this study, we conducted a genome-wide association analysis in rice and detected a major locus, WIDTH OF LEAF AND GRAIN (WLG), that associated with both grain and flag leaf width. WLG encodes a RING-domain E3 ubiquitin ligase. WLGhap.B, which possesses five SNP variations compared to WLGhap.A, encodes a protein with enhanced ubiquitination activity that confers increased rice leaf width and grain size, whereas mutation of WLG leads to narrower leaves and smaller grains. Both WLGhap.A and WLGhap.B interact with LARGE2, a HETC-type E3 ligase, however, WLGhap.B exhibits stronger interaction with LARGE2, thus higher ubiquitination activity towards LARGE2 compared with WLGhap.A. Lysine1021 is crucial for the ubiquitination of LARGE2 by WLG. Loss-of-function of LARGE2 in wlg-1 phenocopies large2-c in grain and leaf width, suggesting that WLG acts upstream of LARGE2. These findings reveal the genetic and molecular mechanism by which the WLG–LARGE2 module mediates grain and leaf size in rice, and suggest the potential of WLGhap.B in improving rice yield.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140821694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Salt stress is an environmental factor that limits plant growth and crop production. With the rapid expansion of salinized arable land worldwide, investigating the molecular mechanisms underlying the salt stress response in plants is urgently needed. Here, we report that GROWTH REGULATING FACTOR 7 (OsGRF7) promotes salt tolerance by regulating arbutin (hydroquinone-β-D-glucopyranoside) metabolism in rice (Oryza sativa). Overexpression of OsGRF7 increased arbutin content, and exogenous arbutin application rescued the salt-sensitive phenotype of OsGRF7 knockdown and knockout plants. OsGRF7 directly promoted the expression of the arbutin biosynthesis genes URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 1 (OsUGT1) and OsUGT5, and knockout of OsUGT1 or OsUGT5 reduced rice arbutin content, salt tolerance, and grain size. Furthermore, OsGRF7 degradation through its interaction with F-BOX AND OTHER DOMAINS CONTAINING PROTEIN 13 (OsFBO13) reduced rice salinity tolerance and grain size. These findings highlight an underexplored role of OsGRF7 in modulating rice arbutin metabolism, salt stress response, and grain size, as well as its broad potential use in rice breeding.
盐胁迫是一种限制植物生长和作物产量的环境因素。随着全球盐碱化耕地的迅速扩大，迫切需要研究植物盐胁迫响应的分子机制。在此，我们报道了生长调节因子 7（OsGRF7）通过调节水稻（Oryza sativa）的熊果苷（对苯二酚-β-D-吡喃葡萄糖苷）代谢促进耐盐性。OsGRF7 的过表达增加了熊果苷的含量，外源熊果苷的应用可挽救 OsGRF7 基因敲除和基因敲除植株的盐敏感表型。OsGRF7 直接促进了熊果苷生物合成基因尿苷二磷酸甘氨酰谷胱甘肽转移酶 1（OsUGT1）和 OsUGT5 的表达，敲除 OsUGT1 或 OsUGT5 会降低水稻熊果苷含量、耐盐性和粒径。此外，OsGRF7 通过与 F-BOX AND OTHER DOMAINS CONTAINING PROTEIN 13（OsFBO13）相互作用而降解，降低了水稻的耐盐性和粒度。这些发现凸显了 OsGRF7 在调节水稻熊果苷代谢、盐胁迫响应和粒度方面尚未被充分探索的作用，以及其在水稻育种中的广泛潜在用途。
{"title":"GROWTH REGULATING FACTOR 7–mediated arbutin metabolism enhances rice salt tolerance","authors":"Yunping Chen, Zhiwu Dan, Shaoqing Li","doi":"10.1093/plcell/koae140","DOIUrl":"https://doi.org/10.1093/plcell/koae140","url":null,"abstract":"Salt stress is an environmental factor that limits plant growth and crop production. With the rapid expansion of salinized arable land worldwide, investigating the molecular mechanisms underlying the salt stress response in plants is urgently needed. Here, we report that GROWTH REGULATING FACTOR 7 (OsGRF7) promotes salt tolerance by regulating arbutin (hydroquinone-β-D-glucopyranoside) metabolism in rice (Oryza sativa). Overexpression of OsGRF7 increased arbutin content, and exogenous arbutin application rescued the salt-sensitive phenotype of OsGRF7 knockdown and knockout plants. OsGRF7 directly promoted the expression of the arbutin biosynthesis genes URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 1 (OsUGT1) and OsUGT5, and knockout of OsUGT1 or OsUGT5 reduced rice arbutin content, salt tolerance, and grain size. Furthermore, OsGRF7 degradation through its interaction with F-BOX AND OTHER DOMAINS CONTAINING PROTEIN 13 (OsFBO13) reduced rice salinity tolerance and grain size. These findings highlight an underexplored role of OsGRF7 in modulating rice arbutin metabolism, salt stress response, and grain size, as well as its broad potential use in rice breeding.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140821839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yutao Zou, Nora Gigli-Bisceglia, Eva van Zelm, Pinelopi Kokkinopoulou, Magdalena M Julkowska, Maarten Besten, Thu-Phuong Nguyen, Hongfei Li, Jasper Lamers, Thijs de Zeeuw, Joram A Dongus, Yuxiao Zeng, Yu Cheng, Iko T Koevoets, Bodil Jørgensen, Marcel Giesbers, Jelmer Vroom, Tijs Ketelaar, Bent Larsen Petersen, Timo Engelsdorf, Joris Sprakel, Yanxia Zhang, Christa Testerink
Soil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploited a real-time salt-induced tilting assay. This assay follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by Na+ ions, but not by osmotic stress. Next, we measured this salt-specific response in 345 natural Arabidopsis (Arabidopsis thaliana) accessions and discovered a genetic locus, encoding the cell wall–modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD) that is associated with root bending in the presence of NaCl (hereafter salt). Extensins are a class of structural cell wall glycoproteins known as hydroxyproline (Hyp)-rich glycoproteins, which are posttranslationally modified by O-glycosylation, mostly involving Hyp-arabinosylation. We show that salt-induced ExAD-dependent Hyp-arabinosylation influences root bending responses and cell wall thickness. Roots of exad1 mutant seedlings, which lack Hyp-arabinosylation of extensin, displayed increased thickness of root epidermal cell walls and greater cell wall porosity. They also showed altered gravitropic root bending in salt conditions and a reduced salt-avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation is a unique salt-specific cellular process required for the directional response of roots exposed to salinity.
{"title":"Arabinosylation of cell wall extensin is required for the directional response to salinity in roots","authors":"Yutao Zou, Nora Gigli-Bisceglia, Eva van Zelm, Pinelopi Kokkinopoulou, Magdalena M Julkowska, Maarten Besten, Thu-Phuong Nguyen, Hongfei Li, Jasper Lamers, Thijs de Zeeuw, Joram A Dongus, Yuxiao Zeng, Yu Cheng, Iko T Koevoets, Bodil Jørgensen, Marcel Giesbers, Jelmer Vroom, Tijs Ketelaar, Bent Larsen Petersen, Timo Engelsdorf, Joris Sprakel, Yanxia Zhang, Christa Testerink","doi":"10.1093/plcell/koae135","DOIUrl":"https://doi.org/10.1093/plcell/koae135","url":null,"abstract":"Soil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploited a real-time salt-induced tilting assay. This assay follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by Na+ ions, but not by osmotic stress. Next, we measured this salt-specific response in 345 natural Arabidopsis (Arabidopsis thaliana) accessions and discovered a genetic locus, encoding the cell wall–modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD) that is associated with root bending in the presence of NaCl (hereafter salt). Extensins are a class of structural cell wall glycoproteins known as hydroxyproline (Hyp)-rich glycoproteins, which are posttranslationally modified by O-glycosylation, mostly involving Hyp-arabinosylation. We show that salt-induced ExAD-dependent Hyp-arabinosylation influences root bending responses and cell wall thickness. Roots of exad1 mutant seedlings, which lack Hyp-arabinosylation of extensin, displayed increased thickness of root epidermal cell walls and greater cell wall porosity. They also showed altered gravitropic root bending in salt conditions and a reduced salt-avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation is a unique salt-specific cellular process required for the directional response of roots exposed to salinity.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Clara Groot Crego, Jaqueline Hess, Gil Yardeni, Marylaure de La Harpe, Clara Priemer, Francesca Beclin, Sarah Saadain, Luiz A Cauz-Santos, Eva M Temsch, Hanna Weiss-Schneeweiss, Michael H J Barfuss, Walter Till, Wolfram Weckwerth, Karolina Heyduk, Christian Lexer, Ovidiu Paun, Thibault Leroy
The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, transposable element (TE) dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species but are not candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.
{"title":"CAM evolution is associated with gene family expansion in an explosive bromeliad radiation","authors":"Clara Groot Crego, Jaqueline Hess, Gil Yardeni, Marylaure de La Harpe, Clara Priemer, Francesca Beclin, Sarah Saadain, Luiz A Cauz-Santos, Eva M Temsch, Hanna Weiss-Schneeweiss, Michael H J Barfuss, Walter Till, Wolfram Weckwerth, Karolina Heyduk, Christian Lexer, Ovidiu Paun, Thibault Leroy","doi":"10.1093/plcell/koae130","DOIUrl":"https://doi.org/10.1093/plcell/koae130","url":null,"abstract":"The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, transposable element (TE) dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species but are not candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"83 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140817590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Photosynthetic control (PCON) is a protective mechanism that prevents light-induced damage to photosystem I (PSI) by ensuring the rate of NADPH and ATP production via linear electron transfer (LET) is balanced by their consumption in the CO2 fixation reactions. Protection of PSI is a priority for plants since they lack a dedicated rapid-repair cycle for this complex, meaning that any damage leads to prolonged photoinhibition and decreased growth. The imbalance between LET and the CO2 fixation reactions is sensed at the level of the transthylakoid ΔpH, which increases when light is in excess. The canonical mechanism of PCON involves feedback control by ΔpH on the plastoquinol oxidation step of LET at cytochrome b6f. PCON thereby maintains the PSI special pair chlorophylls (P700) in an oxidized state, that allows excess electrons unused in the CO2 fixation reactions to be safely quenched via charge recombination. In this review we focus on angiosperms, considering how photo-oxidative damage to PSI comes about, explore the consequences of PSI photoinhibition on photosynthesis and growth, discuss recent progress in understanding PCON regulation, and finally consider the prospects for its future manipulation in crop plants to improve photosynthetic efficiency.
光合控制（PCON）是一种保护机制，通过确保通过线性电子传递（LET）产生的 NADPH 和 ATP 的速率与 CO2 固定反应中的消耗相平衡，从而防止光诱导对光子系统 I（PSI）造成损害。保护 PSI 是植物的当务之急，因为植物缺乏专门针对这一复合体的快速修复循环，这意味着任何损伤都会导致长时间的光抑制和生长衰退。LET 与 CO2 固定反应之间的不平衡可通过转紫函 ΔpH 水平来感知，当光照过量时，ΔpH 会升高。PCON 的典型机制包括 ΔpH 对细胞色素 b6f 中 LET 的质醌氧化步骤的反馈控制。因此，PCON 使 PSI 特殊配对叶绿素（P700）保持氧化状态，从而使二氧化碳固定反应中未使用的多余电子通过电荷重组被安全淬灭。在这篇综述中，我们将以被子植物为研究对象，探讨 PSI 光氧化损伤是如何产生的，探讨 PSI 光抑制对光合作用和生长的影响，讨论在了解 PCON 调节方面的最新进展，最后探讨未来在作物中利用 PCON 提高光合效率的前景。
{"title":"Photosynthetic control at the cytochrome b6f complex","authors":"Gustaf E Degen, Matthew P Johnson","doi":"10.1093/plcell/koae133","DOIUrl":"https://doi.org/10.1093/plcell/koae133","url":null,"abstract":"Photosynthetic control (PCON) is a protective mechanism that prevents light-induced damage to photosystem I (PSI) by ensuring the rate of NADPH and ATP production via linear electron transfer (LET) is balanced by their consumption in the CO2 fixation reactions. Protection of PSI is a priority for plants since they lack a dedicated rapid-repair cycle for this complex, meaning that any damage leads to prolonged photoinhibition and decreased growth. The imbalance between LET and the CO2 fixation reactions is sensed at the level of the transthylakoid ΔpH, which increases when light is in excess. The canonical mechanism of PCON involves feedback control by ΔpH on the plastoquinol oxidation step of LET at cytochrome b6f. PCON thereby maintains the PSI special pair chlorophylls (P700) in an oxidized state, that allows excess electrons unused in the CO2 fixation reactions to be safely quenched via charge recombination. In this review we focus on angiosperms, considering how photo-oxidative damage to PSI comes about, explore the consequences of PSI photoinhibition on photosynthesis and growth, discuss recent progress in understanding PCON regulation, and finally consider the prospects for its future manipulation in crop plants to improve photosynthetic efficiency.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"98 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140651468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, and deubiquitylating enzymes (DUBs) or erasers. DUBs can remove ubiquitin molecules from target proteins. Arabidopsis (A. thaliana) DUBs belong to seven protein families and exhibit a wide range of functions and play an important role in regulating selective protein degradation processes, including proteasomal-, endocytic-, and autophagic protein degradation. DUBs also shape the epigenetic landscape and modulate DNA damage repair processes. In this review, we summarize the current knowledge on DUBs in plants, their cellular functions, and the regulatory mechanisms involved in the spatiotemporal regulation of plant DUBs.
{"title":"Erasing marks: Functions of plant deubiquitylating enzymes in modulating the ubiquitin code","authors":"Karin Vogel, Erika Isono","doi":"10.1093/plcell/koae129","DOIUrl":"https://doi.org/10.1093/plcell/koae129","url":null,"abstract":"Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, and deubiquitylating enzymes (DUBs) or erasers. DUBs can remove ubiquitin molecules from target proteins. Arabidopsis (A. thaliana) DUBs belong to seven protein families and exhibit a wide range of functions and play an important role in regulating selective protein degradation processes, including proteasomal-, endocytic-, and autophagic protein degradation. DUBs also shape the epigenetic landscape and modulate DNA damage repair processes. In this review, we summarize the current knowledge on DUBs in plants, their cellular functions, and the regulatory mechanisms involved in the spatiotemporal regulation of plant DUBs.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140642655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marisa S Otegui, Charlotte Steelheart, Wenlong Ma, Juncai Ma, Byung-Ho Kang, Victor Sanchez De Medina Hernandez, Yasin Dagdas, Caiji Gao, Shino Goto-Yamada, Kazusato Oikawa, Mikio Nishimura
Plants continuously remodel and degrade their organelles due to damage from their metabolic activities and environmental stressors, as well as an integral part of their cell differentiation programs. Whereas certain organelles use local hydrolytic enzymes for limited remodeling, most of pathways that control the partial or complete dismantling of organelles rely on vacuolar degradation. Specifically, selective autophagic pathways play a crucial role in recognizing and sorting plant organelle cargo for vacuolar clearance, especially under cellular stress conditions induced by factors like heat, drought, and damaging light. In these short reviews, we discuss the mechanisms that control the vacuolar degradation of chloroplasts, mitochondria, endoplasmic reticulum, Golgi, and peroxisomes, with an emphasis on autophagy, recently discovered selective autophagy receptors for plant organelles, and crosstalk with other catabolic pathways.
{"title":"Vacuolar Degradation of Plant Organelles","authors":"Marisa S Otegui, Charlotte Steelheart, Wenlong Ma, Juncai Ma, Byung-Ho Kang, Victor Sanchez De Medina Hernandez, Yasin Dagdas, Caiji Gao, Shino Goto-Yamada, Kazusato Oikawa, Mikio Nishimura","doi":"10.1093/plcell/koae128","DOIUrl":"https://doi.org/10.1093/plcell/koae128","url":null,"abstract":"Plants continuously remodel and degrade their organelles due to damage from their metabolic activities and environmental stressors, as well as an integral part of their cell differentiation programs. Whereas certain organelles use local hydrolytic enzymes for limited remodeling, most of pathways that control the partial or complete dismantling of organelles rely on vacuolar degradation. Specifically, selective autophagic pathways play a crucial role in recognizing and sorting plant organelle cargo for vacuolar clearance, especially under cellular stress conditions induced by factors like heat, drought, and damaging light. In these short reviews, we discuss the mechanisms that control the vacuolar degradation of chloroplasts, mitochondria, endoplasmic reticulum, Golgi, and peroxisomes, with an emphasis on autophagy, recently discovered selective autophagy receptors for plant organelles, and crosstalk with other catabolic pathways.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"110 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140642589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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