Plant Molecular Biology最新文献

{"title":"PAP1 and PAP7 are required for association of plastid-encoded RNA polymerase with DNA.","authors":"Joyful Wang, V Miguel Palomar, Ji-Hee Min, Andrzej T Wierzbicki","doi":"10.1007/s11103-024-01498-x","DOIUrl":"10.1007/s11103-024-01498-x","url":null,"abstract":"<p><p>Plastid-encoded RNA polymerase (PEP) is a bacterial-type multisubunit RNA polymerase responsible for the majority of transcription in chloroplasts. PEP consists of four core subunits, which are orthologs of their cyanobacterial counterparts. In Arabidopsis thaliana, PEP is expected to interact with 14 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function are still poorly understood. We used ptChIP-seq to show that PAP1 (also known as pTAC3), a peripheral subunit of PEP, binds to the same genomic loci as RpoB, a core subunit of PEP. The pap1 mutant shows a complete loss of RpoB binding to DNA throughout the genome, indicating that PAP1 is necessary for RpoB binding to DNA. A similar loss of RpoB binding to DNA is observed in a mutant defective in PAP7 (also known as pTAC14), another peripheral PEP subunit. We propose that PAPs are required for the recruitment of core PEP subunits to DNA.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"100"},"PeriodicalIF":3.9,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dormancy regulator Prunus mume DAM6 promotes ethylene-mediated leaf senescence and abscission","authors":"Tzu-Fan Hsiang, Yue-Yu Chen, Ryohei Nakano, Akira Oikawa, Takakazu Matsuura, Yoko Ikeda, Hisayo Yamane","doi":"10.1007/s11103-024-01497-y","DOIUrl":"https://doi.org/10.1007/s11103-024-01497-y","url":null,"abstract":"<p>Leaf senescence and abscission in autumn are critical phenological events in deciduous woody perennials. After leaf fall, dormant buds remain on deciduous woody perennials, which then enter a winter dormancy phase. Thus, leaf fall is widely believed to be linked to the onset of dormancy. In Rosaceae fruit trees, DORMANCY-ASSOCIATED MADS-box (DAM) transcription factors control bud dormancy. However, apart from their regulatory effects on bud dormancy, the biological functions of DAMs have not been thoroughly characterized. In this study, we revealed a novel DAM function influencing leaf senescence and abscission in autumn. In <i>Prunus mume</i>, <i>PmDAM6</i> expression was gradually up-regulated in leaves during autumn toward leaf fall. Our comparative transcriptome analysis using two RNA-seq datasets for the leaves of transgenic plants overexpressing <i>PmDAM6</i> and peach (<i>Prunus persica</i>) <i>DAM6</i> (<i>PpeDAM6</i>) indicated <i>Prunus</i> DAM6 may up-regulate the expression of genes involved in ethylene biosynthesis and signaling as well as leaf abscission. Significant increases in 1-aminocyclopropane-1-carboxylate accumulation and ethylene emission in DEX-treated <i>35S:PmDAM6-GR</i> leaves reflect the inductive effect of PmDAM6 on ethylene biosynthesis. Additionally, ethephon treatments promoted autumn leaf senescence and abscission in apple and <i>P. mume</i>, mirroring the changes due to <i>PmDAM6</i> overexpression. Collectively, these findings suggest that PmDAM6 may induce ethylene emission from leaves, thereby promoting leaf senescence and abscission. This study clarified the effects of <i>Prunus</i> DAM6 on autumn leaf fall, which is associated with bud dormancy onset. Accordingly, in Rosaceae, DAMs may play multiple important roles affecting whole plant growth during the tree dormancy induction phase.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"53 1","pages":""},"PeriodicalIF":5.1,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142251117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"l-Lactate dehydrogenase from Cyanidioschyzon merolae shows high catalytic efficiency for pyruvate reduction and is inhibited by ATP","authors":"Mai Yamamoto, Takashi Osanai, Shoki Ito","doi":"10.1007/s11103-024-01495-0","DOIUrl":"https://doi.org/10.1007/s11103-024-01495-0","url":null,"abstract":"<p><span>l</span>-Lactate is a commodity chemical used in various fields. Microorganisms have produced <span>l</span>-lactate via lactic fermentation using saccharides derived from crops as carbon sources. Recently, <span>l</span>-lactate production using microalgae, whose carbon source is carbon dioxide, has been spotlighted because the prices of the crops have increased. A red alga <i>Cyanidioschyzon merolae</i> produce <span>l</span>-lactate via lactic fermentation under dark anaerobic conditions. The <span>l</span>-lactate titer of <i>C. merolae</i> is higher than those of other microalgae but lower than those of heterotrophic bacteria. Therefore, an increase in the <span>l</span>-lactate titer is required in <i>C. merolae</i>. <span>l</span>-Lactate dehydrogenase (<span>l</span>-LDH) catalyzes the reduction of pyruvate to <span>l</span>-lactate during lactic fermentation. <i>C. merolae</i> possesses five isozymes of <span>l</span>-LDH. The results of previous transcriptome analysis suggested that <span>l</span>-LDHs are the key enzymes in the lactic fermentation of <i>C. merolae</i>. However, their biochemical characteristics, such as catalytic efficiency and tolerance for metabolites, have not been revealed. We compared the amino acid sequences of <i>C. merolae</i> <span>l</span>-LDHs (<i>Cm</i>LDHs) and characterized one of the isozymes, <i>Cm</i>LDH1. BLAST analysis revealed that the sequence similarities of <i>Cm</i>LDH1 and the other isozymes were above 99%. The catalytic efficiency of <i>Cm</i>LDH1 under its optimum conditions was higher than those of <span>l</span>-LDHs of other organisms. ATP decreased the affinity and turnover number of <i>Cm</i>LDH1 for NADH. These findings contribute to understanding the characteristics of <span>l</span>-LDHs of microalgae and the regulatory mechanisms of lactic fermentation in <i>C. merolae</i>.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"18 1","pages":""},"PeriodicalIF":5.1,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association scan reveals the reinforcing effect of nano-potassium in improving the yield and quality of salt-stressed barley via enhancing the antioxidant defense system.","authors":"Samar G Thabet, Fatmah Ahmed Safhi, Andreas Börner, Ahmad M Alqudah","doi":"10.1007/s11103-024-01489-y","DOIUrl":"10.1007/s11103-024-01489-y","url":null,"abstract":"<p><p>Salinity is one of the major environmental factor that can greatly impact the growth, development, and productivity of barley. Our study aims to detect the natural phenotypic variation of morphological and physiological traits under both salinity and potassium nanoparticles (n-K) treatment. In addition to understanding the genetic basis of salt tolerance in barley is a critical aspect of plant breeding for stress resilience. Therefore, a foliar application of n-K was applied at the vegetative stage for 138 barley accessions to enhance salt stress resilience. Interestingly, barley accessions showed high significant increment under n-K treatment compared to saline soil. Based on genome-wide association studies (GWAS) analysis, causative alleles /reliable genomic regions were discovered underlying improved salt resilience through the application of potassium nanoparticles. On chromosome 2H, a highly significant QTN marker (A:C) was located at position 36,665,559 bp which is associated with APX, AsA, GSH, GS, WGS, and TKW under n-K treatment. Inside this region, our candidate gene is HORVU.MOREX.r3.2HG0111480 that annotated as NAC domain protein. Allelic variation detected that the accessions carrying C allele showed higher antioxidants (APX, AsA, and GSH) and barley yield traits (GS, WGS, and TKW) than the accessions carrying A allele, suggesting a positive selection of the accessions carrying C allele that could be used to develop barley varieties with improved salt stress resilience.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"97"},"PeriodicalIF":3.9,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Molecular identification of GAPDHs in cassava highlights the antagonism of MeGAPCs and MeATG8s in plant disease resistance against cassava bacterial blight.","authors":"Hongqiu Zeng, Yanwei Xie, Guoyin Liu, Daozhe Lin, Chaozu He, Haitao Shi","doi":"10.1007/s11103-024-01492-3","DOIUrl":"10.1007/s11103-024-01492-3","url":null,"abstract":"","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"96"},"PeriodicalIF":3.9,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A LBD transcription factor from moso bamboo, PheLBD12, regulates plant height in transgenic rice.","authors":"Min Wu, Yufang Wang, Shunran Zhang, Yan Xiang","doi":"10.1007/s11103-024-01487-0","DOIUrl":"10.1007/s11103-024-01487-0","url":null,"abstract":"<p><p>The regulation mechanism of bamboo height growth has always been one of the hotspots in developmental biology. In the preliminary work of this project, the function of LBD transcription factor regulating height growth was firstly studied. Here, a gene PheLBD12 regulating height growth was screened. PheLBD12-overexpressing transgenic rice had shorter internodes, less bioactive gibberellic acid (GA3), and were more sensitive to GA3 than wild-type (WT) plants, which implied that PheLBD12 involve in gibberellin (GA) pathway. The transcript levels of OsGA2ox3, that encoding GAs deactivated enzyme, was significantly enhanced in PheLBD12-overexpressing transgenic rice. The transcript levels of OsAP2-39, that directly regulating the expression of EUI1 to reduce GA levels, was also significantly enhanced in PheLBD12-overexpressing transgenic rice. Expectedly, yeast one-hybrid assays, Dual-luciferase reporter assay and EMSAs suggested that PheLBD12 directly interacted with the promoter of OsGA2ox3 and OsAP2-39. Together, our results reveal that PheLBD12 regulates plant height growth by modulating GA catabolism. Through the research of this topic, it enriches the research content of LBD transcription factors and it will theoretically enrich the research content of height growth regulation.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"95"},"PeriodicalIF":3.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering physiological and transcriptional mechanisms of maize seed germination.","authors":"Yaqi Jie, Wei Wang, Zishan Wu, Zhaobin Ren, Lu Li, Yuyi Zhou, Mingcai Zhang, Zhaohu Li, Fei Yi, Liusheng Duan","doi":"10.1007/s11103-024-01486-1","DOIUrl":"10.1007/s11103-024-01486-1","url":null,"abstract":"<p><p>Maize is a valuable raw material for feed and food production. Healthy seed germination is important for improving the yield and quality of maize. Seed aging occurs relatively fast in crops and it is a process that delays germination as well as reduces its rate and even causes total loss of seed viability. However, the physiological and transcriptional mechanisms that regulate maize seeds, especially aging seed germination remain unclear. Coronatine (COR) which is a phytotoxin produced by Pseudomonas syringae and a new type of plant growth regulator can effectively regulate plant growth and development, and regulate seed germination. In this study, the physiological and transcriptomic mechanisms of COR-induced maize seed germination under different aging degrees were analyzed. The results showed that 0.001-0.01 μmol/L COR could promote the germination of aging maize seed and the growth of primary roots and shoots. COR treatment increased the content of gibberellins (GA₃) and decreased the content of abscisic acid (ABA) in B73 seeds before germination. The result of RNA-seq analysis showed 497 differentially expressed genes in COR treatment compared with the control. Three genes associated with GA biosynthesis (ZmCPPS2, ZmD3, and ZmGA2ox2), and two genes associated with GA signaling transduction (ZmGID1 and ZmBHLH158) were up-regulated. Three genes negatively regulating GA signaling transduction (ZmGRAS48, ZmGRAS54, and Zm00001d033369) and two genes involved in ABA biosynthesis (ZmVP14 and ZmPCO14472) were down-regulated. The physiological test results also showed that the effects of GA and ABA on seed germination were similar to those of high and low-concentration COR, respectively, which indicated that the effect of COR on seed germination may be carried out through GA and ABA pathways. In addition, GO and KEGG analysis suggested that COR is also highly involved in antioxidant enzyme systems and secondary metabolite synthesis to regulate maize seed germination processes. These findings provide a valuable reference for further research on the mechanisms of maize seed germination.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"94"},"PeriodicalIF":3.9,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142110790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding the plant clock: a review of mathematical models for the circadian regulatory network.","authors":"Shashank Kumar Singh, Ashutosh Srivastava","doi":"10.1007/s11103-024-01493-2","DOIUrl":"10.1007/s11103-024-01493-2","url":null,"abstract":"<p><p>Most organisms have evolved specific mechanisms to respond to changes in environmental conditions such as light and temperature over the course of day. These periodic changes in the physiology and behaviour of organisms, referred to as circadian rhythms, are a consequence of intricate molecular mechanisms in the form of transcription and translational feedback loops. The plant circadian regulatory network is a complex web of interconnected feedback loops involving various transcription factors such as CCA1, LHY, PRRs, TOC1, LUX, ELF3, ELF4, RVE8, and more. This network enables plants to adapt and thrive in diverse environmental conditions. It responds to entrainment signals, including light, temperature, and nutrient concentrations and interacts with most of the physiological functions such as flowering, growth and stress response. Mathematical modelling of these gene regulatory networks enables a deeper understanding of not only the function but also the perturbations that may affect the plant growth and function with changing climate. Over the years, numerous mathematical models have been developed to understand the diverse aspects of plant circadian regulation. In this review, we have delved into the systematic development of these models, outlining the model components and refinements over time. We have also highlighted strengths and limitations of each of the models developed so far. Finally, we conclude the review by describing the prospects for investigation and advancement of these models for better understanding of plant circadian regulation.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"93"},"PeriodicalIF":3.9,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142110791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leaf rolling detection in maize under complex environments using an improved deep learning method.","authors":"Yuanhao Wang, Xuebin Jing, Yonggang Gao, Xiaohong Han, Cheng Zhao, Weihua Pan","doi":"10.1007/s11103-024-01491-4","DOIUrl":"10.1007/s11103-024-01491-4","url":null,"abstract":"<p><p>Leaf rolling is a common adaptive response that plants have evolved to counteract the detrimental effects of various environmental stresses. Gaining insight into the mechanisms underlying leaf rolling alterations presents researchers with a unique opportunity to enhance stress tolerance in crops exhibiting leaf rolling, such as maize. In order to achieve a more profound understanding of leaf rolling, it is imperative to ascertain the occurrence and extent of this phenotype. While traditional manual leaf rolling detection is slow and laborious, research into high-throughput methods for detecting leaf rolling within our investigation scope remains limited. In this study, we present an approach for detecting leaf rolling in maize using the YOLOv8 model. Our method, LRD-YOLO, integrates two significant improvements: a Convolutional Block Attention Module to augment feature extraction capabilities, and a Deformable ConvNets v2 to enhance adaptability to changes in target shape and scale. Through experiments on a dataset encompassing severe occlusion, variations in leaf scale and shape, and complex background scenarios, our approach achieves an impressive mean average precision of 81.6%, surpassing current state-of-the-art methods. Furthermore, the LRD-YOLO model demands only 8.0 G floating point operations and the parameters of 3.48 M. We have proposed an innovative method for leaf rolling detection in maize, and experimental outcomes showcase the efficacy of LRD-YOLO in precisely detecting leaf rolling in complex scenarios while maintaining real-time inference speed.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"92"},"PeriodicalIF":3.9,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11343899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and functional analysis of plant ELO-like elongase for fatty acid elongation.","authors":"Dauenpen Meesapyodsuk, Kaiwen Sun, Xiao Qiu","doi":"10.1007/s11103-024-01490-5","DOIUrl":"10.1007/s11103-024-01490-5","url":null,"abstract":"<p><p>ELO-like elongase is a condensing enzyme elongating long chain fatty acids in eukaryotes. Eranthis hyemalis ELO-like elongase (EhELO1) is the first higher plant ELO-type elongase that is highly active in elongating a wide range of polyunsaturated fatty acids (PUFAs) and some monounsaturated fatty acids (MUFAs). This study attempted using domain swapping and site-directed mutagenesis of EhELO1 and EhELO2, a close homologue of EhELO1 but with no apparent elongase activity, to elucidate the structural determinants critical for catalytic activity and substrate specificity. Domain swapping analysis of the two showed that subdomain B in the C-terminal half of EhELO1 is essential for MUFA elongation while subdomain C in the C-terminal half of EhELO1 is essential for both PUFA and MUFA elongations, implying these regions are critical in defining the architecture of the substrate tunnel for substrate specificity. Site-directed mutagenesis showed that the glycine at position 220 in the subdomain C plays a key role in differentiating the function of the two elongases. In addition, valine at 161 and cysteine at 165 in subdomain A also play critical roles in defining the architecture of the deep substrate tunnel, thereby contributing significantly to the acceptance of, and interaction with primer substrates.</p>","PeriodicalId":20064,"journal":{"name":"Plant Molecular Biology","volume":"114 5","pages":"90"},"PeriodicalIF":3.9,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}