Cyclic electron transport around photosystem I (PSI) is essential for the protection of the photosynthetic apparatus in plants under diverse light conditions. This process is primarily mediated by Proton Gradient Regulation 5 protein/Proton Gradient Regulation 5-like photosynthetic phenotype 1 protein (PGR5/PGRL1) and NADH dehydrogenase-like complex (NDH). In angiosperms, NDH interacts with two PSI complexes through distinct monomeric antennae, LHCA5 and LHCA6, which is crucial for its higher stability under variable light conditions. This interaction represents an advanced evolutionary stage and offers limited insight into the origin of the PSI-NDH supercomplex in evolutionarily older organisms. In contrast, the moss Physcomitrium patens (Pp), which retains the lhca5 gene but lacks the lhca6, offers a glimpse into an earlier evolutionary stage of the PSI-NDH supercomplex. Here we present structural evidence of the Pp PSI-NDH supercomplex formation by single particle electron microscopy, demonstrating the unique ability of Pp to bind a single PSI in two different configurations. One configuration closely resembles the angiosperm model, whereas the other exhibits a novel PSI orientation, rotated clockwise. This structural flexibility in Pp is presumably enabled by the variable incorporation of LHCA5 within PSI and is indicative of an early evolutionary adaptation that allowed for greater diversity at the PSI-NDH interface. Our findings suggest that this variability was reduced as the structural complexity of the NDH complex increased in vascular plants, primarily angiosperms. This study not only clarifies the evolutionary development of PSI-NDH supercomplexes but also highlights the dynamic nature of the adaptive mechanisms of plant photosynthesis.
{"title":"Unique structural attributes of the PSI-NDH supercomplex in Physcomitrium patens.","authors":"Monika Opatíková, Roman Kouřil","doi":"10.1111/tpj.17116","DOIUrl":"https://doi.org/10.1111/tpj.17116","url":null,"abstract":"<p><p>Cyclic electron transport around photosystem I (PSI) is essential for the protection of the photosynthetic apparatus in plants under diverse light conditions. This process is primarily mediated by Proton Gradient Regulation 5 protein/Proton Gradient Regulation 5-like photosynthetic phenotype 1 protein (PGR5/PGRL1) and NADH dehydrogenase-like complex (NDH). In angiosperms, NDH interacts with two PSI complexes through distinct monomeric antennae, LHCA5 and LHCA6, which is crucial for its higher stability under variable light conditions. This interaction represents an advanced evolutionary stage and offers limited insight into the origin of the PSI-NDH supercomplex in evolutionarily older organisms. In contrast, the moss Physcomitrium patens (Pp), which retains the lhca5 gene but lacks the lhca6, offers a glimpse into an earlier evolutionary stage of the PSI-NDH supercomplex. Here we present structural evidence of the Pp PSI-NDH supercomplex formation by single particle electron microscopy, demonstrating the unique ability of Pp to bind a single PSI in two different configurations. One configuration closely resembles the angiosperm model, whereas the other exhibits a novel PSI orientation, rotated clockwise. This structural flexibility in Pp is presumably enabled by the variable incorporation of LHCA5 within PSI and is indicative of an early evolutionary adaptation that allowed for greater diversity at the PSI-NDH interface. Our findings suggest that this variability was reduced as the structural complexity of the NDH complex increased in vascular plants, primarily angiosperms. This study not only clarifies the evolutionary development of PSI-NDH supercomplexes but also highlights the dynamic nature of the adaptive mechanisms of plant photosynthesis.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563455","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}
Na-Na Wang, Ke-Yan Xiu, Min Deng, Qi-Yun Liu, Di-Di Jin, Qiao-Mei Zhao, Huang-Qiang Su, Ting-Ting Qiu, Hai-Yan Wang, Ya-Jun Liu, Xiao-Lan Jiang, Tao Xia, Li-Ping Gao
Monomeric flavan-3-ols and their oligomeric forms, proanthocyanidins (PAs), are closely related to the bitterness of tea beverages. Monomeric flavan-3-ols are characteristic flavor compounds in tea. Increasing the content of PAs and anthocyanins enhances the resistance of tea plants to pathogen invasion but decreases the quality of tea beverages. MATE family transporters play a critical role in transferring monomeric flavan-3-ols and anthocyanins into vacuoles for storage or subsequent condensation into PAs. Their activities modulate the ratio of monomeric flavan-3-ols to PAs and increase anthocyanin content in tea plants. In this study, it was observed that the gene expression and protein phosphorylation level of the MATE transporter CsTT12, a vacuole-localized flavonoid transporter, were notably upregulated following exogenous sucrose treatment, promoting PA synthesis in tea plants. Further analysis revealed that overexpression of CsTT12 and CsTT12S17D significantly increased the content of anthocyanins and PAs in plants, whereas CsTT12S17A did not. In CsTT12 knockdown plants, PA's accumulation decreased significantly, while monomeric catechin content increased. Moreover, phosphorylation modification enhanced the vacuolar membrane localization of CsTT12, whereas dephosphorylation weakened its vacuolar membrane localization. This study uncovers the crucial role of phosphorylation in flavonoid biosynthesis and provides insights into balancing quality improvements and resistance enhancement.
单体黄烷-3-醇及其低聚体形式原花青素(PA)与茶饮料的苦味密切相关。单体黄烷-3-醇是茶叶中特有的风味化合物。增加 PAs 和花青素的含量可增强茶树抵抗病原体入侵的能力,但会降低茶饮料的品质。MATE 家族转运体在将单体黄烷-3-醇和花青素转移到液泡中储存或随后缩合成 PA 方面发挥着关键作用。它们的活动调节了单体黄烷-3-醇与 PA 的比例,增加了茶树中的花青素含量。本研究观察到,外源蔗糖处理后,液泡定位的黄酮类转运体MATE转运体CsTT12的基因表达和蛋白磷酸化水平显著上调,促进了茶树中PA的合成。进一步的分析表明,过表达 CsTT12 和 CsTT12S17D 能显著增加植物中花青素和 PA 的含量,而 CsTT12S17A 则不能。在 CsTT12 基因敲除的植株中,PA 的积累明显减少,而单体儿茶素的含量增加。此外,磷酸化修饰增强了 CsTT12 的液泡膜定位,而去磷酸化则削弱了其液泡膜定位。这项研究揭示了磷酸化在黄酮类化合物生物合成中的关键作用,并为平衡品质改善和提高抗性提供了启示。
{"title":"Effects of phosphorylation on CsTT12 transport function: A comparative phosphoproteomic analysis of flavonoid biosynthesis in tea plants (Camellia sinensis).","authors":"Na-Na Wang, Ke-Yan Xiu, Min Deng, Qi-Yun Liu, Di-Di Jin, Qiao-Mei Zhao, Huang-Qiang Su, Ting-Ting Qiu, Hai-Yan Wang, Ya-Jun Liu, Xiao-Lan Jiang, Tao Xia, Li-Ping Gao","doi":"10.1111/tpj.17120","DOIUrl":"https://doi.org/10.1111/tpj.17120","url":null,"abstract":"<p><p>Monomeric flavan-3-ols and their oligomeric forms, proanthocyanidins (PAs), are closely related to the bitterness of tea beverages. Monomeric flavan-3-ols are characteristic flavor compounds in tea. Increasing the content of PAs and anthocyanins enhances the resistance of tea plants to pathogen invasion but decreases the quality of tea beverages. MATE family transporters play a critical role in transferring monomeric flavan-3-ols and anthocyanins into vacuoles for storage or subsequent condensation into PAs. Their activities modulate the ratio of monomeric flavan-3-ols to PAs and increase anthocyanin content in tea plants. In this study, it was observed that the gene expression and protein phosphorylation level of the MATE transporter CsTT12, a vacuole-localized flavonoid transporter, were notably upregulated following exogenous sucrose treatment, promoting PA synthesis in tea plants. Further analysis revealed that overexpression of CsTT12 and CsTT12<sup>S17D</sup> significantly increased the content of anthocyanins and PAs in plants, whereas CsTT12<sup>S17A</sup> did not. In CsTT12 knockdown plants, PA's accumulation decreased significantly, while monomeric catechin content increased. Moreover, phosphorylation modification enhanced the vacuolar membrane localization of CsTT12, whereas dephosphorylation weakened its vacuolar membrane localization. This study uncovers the crucial role of phosphorylation in flavonoid biosynthesis and provides insights into balancing quality improvements and resistance enhancement.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563443","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}
Tartary buckwheat is known for its ability to adapt to intricate growth conditions and to possess robust stress-resistant properties. Nevertheless, it remains vulnerable to drought stress, which can lead to reduced crop yield. To identify potential genes involved in drought resistance, a genome-wide association study on drought tolerance in Tartary buckwheat germplasm was conducted. A gene encoding pectin methylesterase inhibitors protein (FtPMEI13) was identified, which is not only associated with drought tolerance but also showed induction during drought stress and abscisic acid (ABA) treatment. Further analysis revealed that overexpression of FtPMEI13 leads to improved drought tolerance by altering the activities of antioxidant enzymes and the levels of osmotically active metabolites. Additionally, FtPMEI13 interacts with pectin methylesterase (PME) and inhibits PME activity in response to drought stress. Our results suggest that FtPMEI13 may inhibit the activity of FtPME44/FtPME61, thereby affecting pectin methylesterification in the cell wall and modulating stomatal closure in response to drought stress. Yeast one-hybrid, dual-luciferase assays, and electrophoretic mobility shift assays demonstrated that an ABA-responsive transcription factor FtbZIP46, could bind to the FtPMEI13 promoter, enhancing FtPMEI13 expression. Further analysis indicated that Tartary buckwheat accessions with the genotype resulting in higher FtPMEI13 and FtbZIP46 expression exhibited higher drought tolerance compared to the others. This suggests that this genotype has potential for application in Tartary buckwheat breeding. Furthermore, the natural variation of FtPMEI13 was responsible for decreased drought tolerance during Tartary buckwheat domestication. Taken together, these results provide basic support for Tartary buckwheat breeding for drought tolerance.
{"title":"Genome-wide associated study identifies FtPMEI13 gene conferring drought resistance in Tartary buckwheat.","authors":"Jiayue He, Yanrong Hao, Yuqi He, Wei Li, Yaliang Shi, Muhammad Khurshid, Dili Lai, Chongzhong Ma, Xiangru Wang, Jinbo Li, Jianping Cheng, Alisdair R Fernie, Jingjun Ruan, Kaixuan Zhang, Meiliang Zhou","doi":"10.1111/tpj.17119","DOIUrl":"https://doi.org/10.1111/tpj.17119","url":null,"abstract":"<p><p>Tartary buckwheat is known for its ability to adapt to intricate growth conditions and to possess robust stress-resistant properties. Nevertheless, it remains vulnerable to drought stress, which can lead to reduced crop yield. To identify potential genes involved in drought resistance, a genome-wide association study on drought tolerance in Tartary buckwheat germplasm was conducted. A gene encoding pectin methylesterase inhibitors protein (FtPMEI13) was identified, which is not only associated with drought tolerance but also showed induction during drought stress and abscisic acid (ABA) treatment. Further analysis revealed that overexpression of FtPMEI13 leads to improved drought tolerance by altering the activities of antioxidant enzymes and the levels of osmotically active metabolites. Additionally, FtPMEI13 interacts with pectin methylesterase (PME) and inhibits PME activity in response to drought stress. Our results suggest that FtPMEI13 may inhibit the activity of FtPME44/FtPME61, thereby affecting pectin methylesterification in the cell wall and modulating stomatal closure in response to drought stress. Yeast one-hybrid, dual-luciferase assays, and electrophoretic mobility shift assays demonstrated that an ABA-responsive transcription factor FtbZIP46, could bind to the FtPMEI13 promoter, enhancing FtPMEI13 expression. Further analysis indicated that Tartary buckwheat accessions with the genotype resulting in higher FtPMEI13 and FtbZIP46 expression exhibited higher drought tolerance compared to the others. This suggests that this genotype has potential for application in Tartary buckwheat breeding. Furthermore, the natural variation of FtPMEI13 was responsible for decreased drought tolerance during Tartary buckwheat domestication. Taken together, these results provide basic support for Tartary buckwheat breeding for drought tolerance.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563444","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}
Jorge Fung-Uceda, María Sol Gómez, Laura Rodríguez-Casillas, Anna González-Gil, Crisanto Gutierrez
Rhythmic oscillation of biological processes helps organisms adapt their physiological responses to the most appropriate time of the day. Chromatin remodeling has been described as one of the molecular mechanisms controlling these oscillations. The importance of these changes in transcriptional activation as well as in the maintenance of heterochromatic regions has been widely demonstrated. However, little is still known on how diurnal changes can impact the global status of chromatin modifications and, hence, control gene expression. In plants, the repressive mark H3K27me1, deposited by ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 and 6 (ATXR5 and 6) methyltransferases, is largely associated with transposable elements but also covers lowly expressed genes. Here we show that this histone modification is preferentially deposited during the night. In euchromatic regions, it is found along the bodies of DNA damage response genes (DDR), where it is needed for their proper expression. The absence of H3K27me1 translates into an enhanced expression of DDR genes that follows a rhythmic oscillation pattern. This evidences a link between chromatin modifications and their synchronization with the diurnal cycle in order to accurately modulate the activation of biological processes to the most appropriate time of the day.
生物过程的节律振荡有助于生物体根据一天中最合适的时间调整其生理反应。染色质重塑被描述为控制这些振荡的分子机制之一。这些变化在转录激活和维持异染色质区域方面的重要性已得到广泛证实。然而,人们对昼夜变化如何影响染色质修饰的整体状态并进而控制基因表达仍然知之甚少。在植物中,抑制性标记 H3K27me1 由 ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 和 6(ATXR5 和 6)甲基转移酶沉积,主要与转座元件相关,但也覆盖低表达基因。我们在这里发现,这种组蛋白修饰在夜间优先沉积。在外显子区域,它沿着 DNA 损伤应答基因(DDR)的主体被发现,这些基因的正常表达需要它。H3K27me1 的缺失会导致 DDR 基因的表达增强,并呈现出有节奏的振荡模式。这证明了染色质修饰与昼夜周期同步之间的联系,以便在一天中最合适的时间准确调节生物过程的激活。
{"title":"Diurnal control of H3K27me1 deposition shapes expression of a subset of cell cycle and DNA damage response genes.","authors":"Jorge Fung-Uceda, María Sol Gómez, Laura Rodríguez-Casillas, Anna González-Gil, Crisanto Gutierrez","doi":"10.1111/tpj.17114","DOIUrl":"https://doi.org/10.1111/tpj.17114","url":null,"abstract":"<p><p>Rhythmic oscillation of biological processes helps organisms adapt their physiological responses to the most appropriate time of the day. Chromatin remodeling has been described as one of the molecular mechanisms controlling these oscillations. The importance of these changes in transcriptional activation as well as in the maintenance of heterochromatic regions has been widely demonstrated. However, little is still known on how diurnal changes can impact the global status of chromatin modifications and, hence, control gene expression. In plants, the repressive mark H3K27me1, deposited by ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 and 6 (ATXR5 and 6) methyltransferases, is largely associated with transposable elements but also covers lowly expressed genes. Here we show that this histone modification is preferentially deposited during the night. In euchromatic regions, it is found along the bodies of DNA damage response genes (DDR), where it is needed for their proper expression. The absence of H3K27me1 translates into an enhanced expression of DDR genes that follows a rhythmic oscillation pattern. This evidences a link between chromatin modifications and their synchronization with the diurnal cycle in order to accurately modulate the activation of biological processes to the most appropriate time of the day.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563441","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}
Qi Mu, Jialu Wei, Hallie K Longest, Hua Liu, Si Nian Char, Jacob T Hinrichsen, Laura E Tibbs-Cortes, Gregory R Schoenbaum, Bing Yang, Xianran Li, Jianming Yu
Manipulating plant height is an essential component of crop improvement. Plant height was generally reduced through breeding in wheat, rice, and sorghum to resist lodging and increase grain yield but kept high for bioenergy crops. Here, we positionally cloned a plant height quantitative trait locus (QTL) qHT7.1 as a MYB transcription factor controlling internode elongation, cell proliferation, and cell morphology in sorghum. A 740 bp transposable element insertion in the intronic region caused a partial mis-splicing event, generating a novel transcript that included an additional exon and a premature stop codon, leading to short plant height. The dominant allele had an overall higher expression than the recessive allele across development and internode position, while both alleles' expressions peaked at 46 days after planting and progressively decreased from the top to lower internodes. The orthologue of qHT7.1 was identified to underlie the brachytic1 (br1) locus in maize. A large insertion in exon 3 and a 160 bp insertion at the promoter region were identified in the br1 mutant, while an 18 bp promoter insertion was found to be associated with reduced plant height in a natural recessive allele. CRISPR/Cas9-induced gene knockout of br1 in two maize inbred lines showed significant plant height reduction. These findings revealed functional connections across natural, mutant, and edited alleles of this MYB transcription factor in sorghum and maize. This enriched our understanding of plant height regulation and enhanced our toolbox for fine-tuning plant height for crop improvement.
控制株高是作物改良的重要组成部分。小麦、水稻和高粱的育种通常会降低株高以抗倒伏和增加谷物产量,但生物能源作物的育种则会保持较高的株高。在这里,我们定位克隆了一个株高数量性状位点(QTL)qHT7.1,它是一个控制高粱节间伸长、细胞增殖和细胞形态的 MYB 转录因子。内含子区域的 740 bp 转座元件插入引起了部分错误剪接事件,产生了一个包含额外外显子和过早终止密码子的新转录本,导致植株矮小。显性等位基因在整个发育过程和节间位置上的表达量总体高于隐性等位基因,而两个等位基因的表达量都在播种后 46 天达到峰值,并从节间顶部到下部逐渐降低。qHT7.1的直向同源物被确定为玉米brachytic1(br1)基因座的基础。在 br1 突变体中发现了外显子 3 中的大插入和启动子区域的 160 bp 插入,而在自然隐性等位基因中发现 18 bp 启动子插入与植株高度降低有关。在两个玉米近交系中,CRISPR/Cas9诱导的br1基因敲除显示植株高度显著降低。这些发现揭示了高粱和玉米中这种 MYB 转录因子的天然、突变和编辑等位基因之间的功能联系。这丰富了我们对植株高度调控的理解,增强了我们微调植株高度以改良作物的工具箱。
{"title":"A MYB transcription factor underlying plant height in sorghum qHT7.1 and maize Brachytic 1 loci.","authors":"Qi Mu, Jialu Wei, Hallie K Longest, Hua Liu, Si Nian Char, Jacob T Hinrichsen, Laura E Tibbs-Cortes, Gregory R Schoenbaum, Bing Yang, Xianran Li, Jianming Yu","doi":"10.1111/tpj.17111","DOIUrl":"https://doi.org/10.1111/tpj.17111","url":null,"abstract":"<p><p>Manipulating plant height is an essential component of crop improvement. Plant height was generally reduced through breeding in wheat, rice, and sorghum to resist lodging and increase grain yield but kept high for bioenergy crops. Here, we positionally cloned a plant height quantitative trait locus (QTL) qHT7.1 as a MYB transcription factor controlling internode elongation, cell proliferation, and cell morphology in sorghum. A 740 bp transposable element insertion in the intronic region caused a partial mis-splicing event, generating a novel transcript that included an additional exon and a premature stop codon, leading to short plant height. The dominant allele had an overall higher expression than the recessive allele across development and internode position, while both alleles' expressions peaked at 46 days after planting and progressively decreased from the top to lower internodes. The orthologue of qHT7.1 was identified to underlie the brachytic1 (br1) locus in maize. A large insertion in exon 3 and a 160 bp insertion at the promoter region were identified in the br1 mutant, while an 18 bp promoter insertion was found to be associated with reduced plant height in a natural recessive allele. CRISPR/Cas9-induced gene knockout of br1 in two maize inbred lines showed significant plant height reduction. These findings revealed functional connections across natural, mutant, and edited alleles of this MYB transcription factor in sorghum and maize. This enriched our understanding of plant height regulation and enhanced our toolbox for fine-tuning plant height for crop improvement.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562625","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}
Pub Date : 2024-11-01Epub Date: 2024-10-10DOI: 10.1111/tpj.17068
Xiaofang Yi, Congcong Wang, Xiaoqi Yuan, Mi Zhang, Changwei Zhang, Tiaojiao Qin, Haiyun Wang, Liang Xu, Liwang Liu, Yan Wang
Radish (Raphanus sativus L.) is one of the most important root vegetable crops worldwide. However, gene function exploration and germplasm innovation still face tremendous challenges due to its extremely low transformation efficiency. Here, an economic and highly efficient genetic transformation method for radish was explored by Agrobacterium rhizogenes-mediated transformation with the help of combining special developmental regulator (DR) genes and the visual identification reporter. Firstly, the RUBY gene, a betalain biosynthesis system, could result in a visual red-violet color used as a convenient and effective reporter for monitoring transgenic hairy roots screening of radish. However, the hairy roots-to-shoots conversion system of radish still stands as a barrier to the obtainment of whole transgenic plants, although different hormone combinations and various culture conditions were tried. Following, two DR genes including Wuschel2 (Wus2) and isopentenyl transferase (ipt), as well as their combination Wus2-ipt were introduced for the shoot regeneration capacity improvement. The results showed that the transgenic shoots could be directly generated without externally supplying any hormones in the presence of a Wus2-ipt combination. Then, Wus2-ipt along with the RUBY reporter was employed to establish an efficient genetic transformation system of radish. Moreover, this system was applied in generating gene-edited radish plants and the phytoene desaturase (RsPDS) gene was effectively knockout through albino phenotype observation and sequencing analysis. These findings have the potential to be widely applied in genetic transformation and genome-editing genetic improvement of other vegetable species.
{"title":"Exploring an economic and highly efficient genetic transformation and genome-editing system for radish through developmental regulators and visible reporter.","authors":"Xiaofang Yi, Congcong Wang, Xiaoqi Yuan, Mi Zhang, Changwei Zhang, Tiaojiao Qin, Haiyun Wang, Liang Xu, Liwang Liu, Yan Wang","doi":"10.1111/tpj.17068","DOIUrl":"10.1111/tpj.17068","url":null,"abstract":"<p><p>Radish (Raphanus sativus L.) is one of the most important root vegetable crops worldwide. However, gene function exploration and germplasm innovation still face tremendous challenges due to its extremely low transformation efficiency. Here, an economic and highly efficient genetic transformation method for radish was explored by Agrobacterium rhizogenes-mediated transformation with the help of combining special developmental regulator (DR) genes and the visual identification reporter. Firstly, the RUBY gene, a betalain biosynthesis system, could result in a visual red-violet color used as a convenient and effective reporter for monitoring transgenic hairy roots screening of radish. However, the hairy roots-to-shoots conversion system of radish still stands as a barrier to the obtainment of whole transgenic plants, although different hormone combinations and various culture conditions were tried. Following, two DR genes including Wuschel2 (Wus2) and isopentenyl transferase (ipt), as well as their combination Wus2-ipt were introduced for the shoot regeneration capacity improvement. The results showed that the transgenic shoots could be directly generated without externally supplying any hormones in the presence of a Wus2-ipt combination. Then, Wus2-ipt along with the RUBY reporter was employed to establish an efficient genetic transformation system of radish. Moreover, this system was applied in generating gene-edited radish plants and the phytoene desaturase (RsPDS) gene was effectively knockout through albino phenotype observation and sequencing analysis. These findings have the potential to be widely applied in genetic transformation and genome-editing genetic improvement of other vegetable species.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":"1682-1692"},"PeriodicalIF":5.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142454412","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}
Pub Date : 2024-11-01Epub Date: 2024-10-09DOI: 10.1111/tpj.17053
Ladislav Hodač, Kevin Karbstein, Lara Kösters, Michael Rzanny, Hans Christian Wittich, David Boho, David Šubrt, Patrick Mäder, Jana Wäldchen
Plant leaves play a pivotal role in automated species identification using deep learning (DL). However, achieving reproducible capture of leaf variation remains challenging due to the inherent "black box" problem of DL models. To evaluate the effectiveness of DL in capturing leaf shape, we used geometric morphometrics (GM), an emerging component of eXplainable Artificial Intelligence (XAI) toolkits. We photographed Ranunculus auricomus leaves directly in situ and after herbarization. From these corresponding leaf images, we automatically extracted DL features using a neural network and digitized leaf shapes using GM. The association between the extracted DL features and GM shapes was then evaluated using dimension reduction and covariation models. DL features facilitated the clustering of leaf images by source populations in both in situ and herbarized leaf image datasets, and certain DL features were significantly associated with biological leaf shape variation as inferred by GM. DL features also enabled leaf classification into morpho-phylogenomic groups within the intricate R. auricomus species complex. We demonstrated that simple in situ leaf imaging and DL reproducibly captured leaf shape variation at the population level, while combining this approach with GM provided key insights into the shape information extracted from images by computer vision, a necessary prerequisite for reliable automated plant phenotyping.
{"title":"Deep learning to capture leaf shape in plant images: Validation by geometric morphometrics.","authors":"Ladislav Hodač, Kevin Karbstein, Lara Kösters, Michael Rzanny, Hans Christian Wittich, David Boho, David Šubrt, Patrick Mäder, Jana Wäldchen","doi":"10.1111/tpj.17053","DOIUrl":"10.1111/tpj.17053","url":null,"abstract":"<p><p>Plant leaves play a pivotal role in automated species identification using deep learning (DL). However, achieving reproducible capture of leaf variation remains challenging due to the inherent \"black box\" problem of DL models. To evaluate the effectiveness of DL in capturing leaf shape, we used geometric morphometrics (GM), an emerging component of eXplainable Artificial Intelligence (XAI) toolkits. We photographed Ranunculus auricomus leaves directly in situ and after herbarization. From these corresponding leaf images, we automatically extracted DL features using a neural network and digitized leaf shapes using GM. The association between the extracted DL features and GM shapes was then evaluated using dimension reduction and covariation models. DL features facilitated the clustering of leaf images by source populations in both in situ and herbarized leaf image datasets, and certain DL features were significantly associated with biological leaf shape variation as inferred by GM. DL features also enabled leaf classification into morpho-phylogenomic groups within the intricate R. auricomus species complex. We demonstrated that simple in situ leaf imaging and DL reproducibly captured leaf shape variation at the population level, while combining this approach with GM provided key insights into the shape information extracted from images by computer vision, a necessary prerequisite for reliable automated plant phenotyping.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":"1343-1357"},"PeriodicalIF":5.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386823","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}
Yunjuan Ren, Ziyu Zhang, Diana Zhanakhmetova, Wenhui Li, Shaolin Chen, Tomáš Werner, Johannes Liesche
The rate of sucrose export from leaves is a major factor in balancing whole-plant carbon and energy partitioning. A comprehensive study of its dynamics and relationship to photosynthesis, sink demand, and other relevant processes is hampered by the shortcomings of current methods for measuring sucrose phloem loading. We utilize the ability of sucrose transporter proteins, known as SUCs or SUTs, to specifically transport the fluorescent molecule esculin in a novel assay to measure phloem loading rates. Esculin was administered to source leaves and its fluorescence in the leaf extract was measured after 1 or 2 h. Dicot plants with an active phloem loading strategy showed an export-dependent reduction of esculin fluorescence. Relative leaf esculin export rates correlated with leaf export rates of isotopic carbon and phloem exudate sucrose levels. We used esculin experiments to examine the effects of phytohormones on phloem loading in Arabidopsis, showing, for example, that auxin induces phloem loading while cytokinin reduces it. Transcriptional regulation of AtSUC2 by AUXIN RESPONSE FACTOR1 (ARF1) corroborated the link between auxin signaling and phloem loading. Unlike established methods, the esculin assay is rapid and does not require specialized equipment. Potential applications and limitations of the esculin assay are discussed.
{"title":"Fast and simple fluorometric measurement of phloem loading exposes auxin-dependent regulation of Arabidopsis sucrose transporter AtSUC2.","authors":"Yunjuan Ren, Ziyu Zhang, Diana Zhanakhmetova, Wenhui Li, Shaolin Chen, Tomáš Werner, Johannes Liesche","doi":"10.1111/tpj.17110","DOIUrl":"https://doi.org/10.1111/tpj.17110","url":null,"abstract":"<p><p>The rate of sucrose export from leaves is a major factor in balancing whole-plant carbon and energy partitioning. A comprehensive study of its dynamics and relationship to photosynthesis, sink demand, and other relevant processes is hampered by the shortcomings of current methods for measuring sucrose phloem loading. We utilize the ability of sucrose transporter proteins, known as SUCs or SUTs, to specifically transport the fluorescent molecule esculin in a novel assay to measure phloem loading rates. Esculin was administered to source leaves and its fluorescence in the leaf extract was measured after 1 or 2 h. Dicot plants with an active phloem loading strategy showed an export-dependent reduction of esculin fluorescence. Relative leaf esculin export rates correlated with leaf export rates of isotopic carbon and phloem exudate sucrose levels. We used esculin experiments to examine the effects of phytohormones on phloem loading in Arabidopsis, showing, for example, that auxin induces phloem loading while cytokinin reduces it. Transcriptional regulation of AtSUC2 by AUXIN RESPONSE FACTOR1 (ARF1) corroborated the link between auxin signaling and phloem loading. Unlike established methods, the esculin assay is rapid and does not require specialized equipment. Potential applications and limitations of the esculin assay are discussed.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562627","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}
Plant trichomes are an excellent model for studying cell differentiation and development, providing crucial defenses against biotic and abiotic stresses. There is a well-established inverse relationship between trichome density and aphid prevalence, indicating that higher trichome density leads to reduced aphid infestations. Here we present the cloning and characterization of a dominant quantitative trait locus, HIC (hirsute cotton), which significantly enhances cotton trichome density. This enhancement leads to markedly improved resistance against cotton aphids. The HIC encodes an HD-ZIP IV transcriptional activator, crucial for trichome initiation. Overexpression of HIC leads to a substantial increase in trichome density, while knockdown of HIC results in a marked decrease in density, confirming its role in trichome regulation. We identified a variant in the HIC promoter (-810 bp A to C) that increases transcription of HIC and trichome density in hirsute cotton compared with Gossypium hirsutum cultivars with fewer or no trichomes. Interestingly, although the -810 variant in the HIC promoter is the same in G. barbadense and hirsute cotton, the presence of a copia-like retrotransposon insertion in the coding region of HIC in G. barbadense causes premature transcription termination. Further analysis revealed that HIC positively regulates trichome density by directly targeting the EXPANSIN A2 gene, which is involved in cell wall development. Taken together, our results underscore the pivotal function of HIC as a primary regulator during the initial phases of trichome formation, and its prospective utility in enhancing aphid resistance in superior cotton cultivars via selective breeding.
植物毛状体是研究细胞分化和发育的绝佳模型,可提供抵御生物和非生物胁迫的重要防御能力。毛状体密度与蚜虫发生率之间存在着公认的反比关系,表明毛状体密度越高,蚜虫发生率越低。在这里,我们展示了一个显性数量性状基因座 HIC(多毛棉花)的克隆和特征描述,该基因座能显著提高棉花的毛状体密度。这种增强显著提高了对棉蚜的抗性。HIC 编码一个 HD-ZIP IV 转录激活子,对毛状体的启动至关重要。过量表达 HIC 会导致毛状体密度大幅增加,而敲除 HIC 则会导致密度明显降低,这证实了它在毛状体调控中的作用。我们在 HIC 启动子中发现了一个变体(-810 bp A 到 C),与毛状体较少或没有毛状体的长硬毛棉花栽培品种相比,它能增加 HIC 的转录和毛状体密度。有趣的是,虽然 HIC 启动子中的 -810 变体在长硬毛棉花和长硬毛棉花中是相同的,但在长硬毛棉花中,HIC 编码区中 copia 样逆转录质子插入会导致转录过早终止。进一步的分析表明,HIC 通过直接靶向参与细胞壁发育的 EXPANSIN A2 基因对毛状体密度进行正向调节。综上所述,我们的研究结果强调了 HIC 作为毛状体形成初期的主要调控因子的关键功能,以及它在通过选择性育种提高优良棉花品种抗蚜虫能力方面的应用前景。
{"title":"Natural variation at the cotton HIC locus increases trichome density and enhances resistance to aphids.","authors":"Yanan Wang, Qi Zhou, Jilong Zhang, Haiyan He, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang, Chengzhen Liang","doi":"10.1111/tpj.17050","DOIUrl":"10.1111/tpj.17050","url":null,"abstract":"<p><p>Plant trichomes are an excellent model for studying cell differentiation and development, providing crucial defenses against biotic and abiotic stresses. There is a well-established inverse relationship between trichome density and aphid prevalence, indicating that higher trichome density leads to reduced aphid infestations. Here we present the cloning and characterization of a dominant quantitative trait locus, HIC (hirsute cotton), which significantly enhances cotton trichome density. This enhancement leads to markedly improved resistance against cotton aphids. The HIC encodes an HD-ZIP IV transcriptional activator, crucial for trichome initiation. Overexpression of HIC leads to a substantial increase in trichome density, while knockdown of HIC results in a marked decrease in density, confirming its role in trichome regulation. We identified a variant in the HIC promoter (-810 bp A to C) that increases transcription of HIC and trichome density in hirsute cotton compared with Gossypium hirsutum cultivars with fewer or no trichomes. Interestingly, although the -810 variant in the HIC promoter is the same in G. barbadense and hirsute cotton, the presence of a copia-like retrotransposon insertion in the coding region of HIC in G. barbadense causes premature transcription termination. Further analysis revealed that HIC positively regulates trichome density by directly targeting the EXPANSIN A2 gene, which is involved in cell wall development. Taken together, our results underscore the pivotal function of HIC as a primary regulator during the initial phases of trichome formation, and its prospective utility in enhancing aphid resistance in superior cotton cultivars via selective breeding.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":" ","pages":"1304-1316"},"PeriodicalIF":5.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370462","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>Hydathodes are organs on the leaves of all vascular plants. They regulate the secretion of fluids derived from the xylem sap (Bellenot et al., <span>2022</span>; Cerutti et al., <span>2019</span>). When stomata are closed at night and the humidity level levels are too high, the xylem delivers excess water from the roots, which is secreted at the hydathodes in a process called guttation (Figure 1a) (Singh, <span>2020</span>). Hydathodes are composed of an epidermal surface layer with water pores, and an inner parenchyma, called the epithem, which is highly vascularized and constitutes a direct connection between leaf surface and xylem vessels (Figure 1b) (Bellenot et al., <span>2022</span>). Hydathodes were first described by the German botanist Anton de Bary in 1877, and named by the Austrian botanist Gottlieb Haberlandt in 1897, from the Greek ‘hyda’ (water) and ‘hodos’ (way) (Bellenot et al., <span>2022</span>). When Jean-Marc Routaboul, the corresponding author of the highlighted publication, joined Laurent Noël's team at INRAE, France, in 2018, he was surprised to find that hydathodes and the process of guttation were not well understood at the molecular level. Therefore, Routaboul and his colleagues set out to test two long-standing hypotheses about hydathodes: that hydathodes are sites of auxin accumulation, and that they facilitate the withholding of nutrients from guttation fluids (Routaboul et al., <span>2024</span>).</p><p>These hypotheses are based on genes expressed in hydathodes, including those for auxin biosynthesis, transport, and signalling. Moreover, the presence of auxin in hydathodes was detected by antibodies and by using the auxin signalling reporter <i>DR5</i> (Aloni et al., <span>2003</span>). Other hydathode-specific genes encode membrane transporters for amino acids, sugar or ions (Nagai et al., <span>2013</span>), potentially preventing nutrient loss through guttation. For their study, Routaboul <i>et al</i>. combined RNAseq of hydathode-enriched tissue by deep sequencing with a detailed metabolomic analysis of guttation fluids.</p><p>First, the authors compared the transcriptome of macro-dissected leaf margins containing hydathodes with the transcriptome of leaf blade tissue of mature Arabidopsis leaves. They found higher expression of genes related to auxin metabolism, stress, DNA, plant cell wall, transport, RNA and lipids in the hydathode-enriched tissue. Genes related to glucosinolate synthesis and transport, the sulfation pathway, metal handling or photosynthesis were more highly expressed in the leaf blade. Because many genes related to auxin biosynthesis were expressed in hydathodes, the authors measured the accumulation of free auxin in hydathode-enriched tissue and leaf blades with liquid chromatography/mass spectrometry (LC/MS) and found nearly 40% more free auxin in hydathode-enriched tissue than in leaf blades. Reporter gene expression confirmed that genes encoding the key auxin biosynthetic enzymes Tryp
{"title":"Exit control: the role of Arabidopsis hydathodes in auxin storage and nutrient recovery","authors":"Gwendolyn Kirschner","doi":"10.1111/tpj.17118","DOIUrl":"10.1111/tpj.17118","url":null,"abstract":"<p>Hydathodes are organs on the leaves of all vascular plants. They regulate the secretion of fluids derived from the xylem sap (Bellenot et al., <span>2022</span>; Cerutti et al., <span>2019</span>). When stomata are closed at night and the humidity level levels are too high, the xylem delivers excess water from the roots, which is secreted at the hydathodes in a process called guttation (Figure 1a) (Singh, <span>2020</span>). Hydathodes are composed of an epidermal surface layer with water pores, and an inner parenchyma, called the epithem, which is highly vascularized and constitutes a direct connection between leaf surface and xylem vessels (Figure 1b) (Bellenot et al., <span>2022</span>). Hydathodes were first described by the German botanist Anton de Bary in 1877, and named by the Austrian botanist Gottlieb Haberlandt in 1897, from the Greek ‘hyda’ (water) and ‘hodos’ (way) (Bellenot et al., <span>2022</span>). When Jean-Marc Routaboul, the corresponding author of the highlighted publication, joined Laurent Noël's team at INRAE, France, in 2018, he was surprised to find that hydathodes and the process of guttation were not well understood at the molecular level. Therefore, Routaboul and his colleagues set out to test two long-standing hypotheses about hydathodes: that hydathodes are sites of auxin accumulation, and that they facilitate the withholding of nutrients from guttation fluids (Routaboul et al., <span>2024</span>).</p><p>These hypotheses are based on genes expressed in hydathodes, including those for auxin biosynthesis, transport, and signalling. Moreover, the presence of auxin in hydathodes was detected by antibodies and by using the auxin signalling reporter <i>DR5</i> (Aloni et al., <span>2003</span>). Other hydathode-specific genes encode membrane transporters for amino acids, sugar or ions (Nagai et al., <span>2013</span>), potentially preventing nutrient loss through guttation. For their study, Routaboul <i>et al</i>. combined RNAseq of hydathode-enriched tissue by deep sequencing with a detailed metabolomic analysis of guttation fluids.</p><p>First, the authors compared the transcriptome of macro-dissected leaf margins containing hydathodes with the transcriptome of leaf blade tissue of mature Arabidopsis leaves. They found higher expression of genes related to auxin metabolism, stress, DNA, plant cell wall, transport, RNA and lipids in the hydathode-enriched tissue. Genes related to glucosinolate synthesis and transport, the sulfation pathway, metal handling or photosynthesis were more highly expressed in the leaf blade. Because many genes related to auxin biosynthesis were expressed in hydathodes, the authors measured the accumulation of free auxin in hydathode-enriched tissue and leaf blades with liquid chromatography/mass spectrometry (LC/MS) and found nearly 40% more free auxin in hydathode-enriched tissue than in leaf blades. Reporter gene expression confirmed that genes encoding the key auxin biosynthetic enzymes Tryp","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"120 3","pages":"855-856"},"PeriodicalIF":6.2,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.17118","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542443","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}