Molecular Plant最新文献_第3页

Reevaluating statistical methods in metabolomic studies: A case for Spearman's correlation. 代谢组学研究中统计方法的重新评估：一个Spearman相关的案例。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2024-12-24 DOI: 10.1016/j.molp.2024.12.014

Yoshiyasu Takefuji

引用次数: 0

Activation and memory of the heat shock response is mediated by prion-like domains of sensory HSFs in Arabidopsis. 拟南芥热休克反应的激活和记忆是由感觉hsf的朊蛋白样结构域介导的。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-09 DOI: 10.1016/j.molp.2025.01.007

Maolin Peng, Katja E Jaeger, Yunlong Lu, Zhuping Fan, Wei Zeng, Arun Sampathkumar, Philip A Wigge

{"title":"Activation and memory of the heat shock response is mediated by prion-like domains of sensory HSFs in Arabidopsis.","authors":"Maolin Peng, Katja E Jaeger, Yunlong Lu, Zhuping Fan, Wei Zeng, Arun Sampathkumar, Philip A Wigge","doi":"10.1016/j.molp.2025.01.007","DOIUrl":"10.1016/j.molp.2025.01.007","url":null,"abstract":"Plants are able to sense and remember heat stress. An initial priming heat stress enables plants to acclimate so that they are able to survive a subsequent higher temperature. The heat shock transcription factors (HSFs) play a crucial role in this process, but the mechanisms by which plants sense heat stress are not well understood. By comprehensively analyzing the binding targets of all the HSFs, we found that HSFs act in a network, with upstream sensory HSFs acting in a transcriptional cascade to activate downstream HSFs and protective proteins. The upstream sensory HSFs are activated by heat at the protein level via a modular prion-like domain (PrD) structure. PrD1 enables HSF sequestration via chaperone binding, allowing release under heat shock. Activated HSFs are recruited into transcriptionally active foci via PrD2, enabling the formation of DNA loops between heat-responsive promoters and enhancer motifs, boosting gene expression days after a priming heat stress. The ability of HSFs to respond rapidly to heat via a protein phase-change response is likely a conserved mechanism in eukaryotes.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"457-467"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142952128","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}

引用次数: 0

GEFormer: A genotype-environment interaction-based genomic prediction method that integrates the gating multilayer perceptron and linear attention mechanisms.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-28 DOI: 10.1016/j.molp.2025.01.020

Zhou Yao, Mengting Yao, Chuang Wang, Ke Li, Junhao Guo, Yingjie Xiao, Jianbing Yan, Jianxiao Liu

{"title":"GEFormer: A genotype-environment interaction-based genomic prediction method that integrates the gating multilayer perceptron and linear attention mechanisms.","authors":"Zhou Yao, Mengting Yao, Chuang Wang, Ke Li, Junhao Guo, Yingjie Xiao, Jianbing Yan, Jianxiao Liu","doi":"10.1016/j.molp.2025.01.020","DOIUrl":"10.1016/j.molp.2025.01.020","url":null,"abstract":"The integration of genotypic and environmental data can enhance genomic prediction accuracy for crop field traits. Existing genomic prediction methods fail to consider environmental factors and the real growth environments of crops, resulting in low genomic prediction accuracy. In this work, we developed GEFormer, a genotype-environment interaction genomic prediction method that integrates gating multilayer perceptron (gMLP) and linear attention mechanisms. First, GEFormer uses gMLP to extract local and global features among SNPs. Then, Omni-dimensional Dynamic Convolution is used to extract the dynamic and comprehensive features of multiple environmental factors within each day, taking into consideration the real growth pattern of crops. A linear attention mechanism is used to capture the temporal features of environmental changes. Finally, GEFormer uses a gating mechanism to effectively fuse the genomic and environmental features. We examined the accuracy of GEFormer for predicting important agronomic traits of maize, rice, and wheat under three experimental scenarios: untested genotypes in tested environments, tested genotypes in untested environments, and untested genotypes in untested environments. The results showed that GEFormer outperforms six cutting-edge statistical learning methods and four machine learning methods, especially with great advantages under the scenario of untested genotypes in untested environments. In addition, we used GEFormer for three real-world breeding applications: phenotype prediction in unknown environments, hybrid phenotype prediction using an inbred population, and cross-population phenotype prediction. The results showed that GEFormer had better prediction performance in actual breeding scenarios and could be used to assist in crop breeding.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"527-549"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066845","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}

引用次数: 0

Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid. 基因组学、转录组学和代谢组学分析揭示了达尔文兰花的肟生物合成趋同进化。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2024-12-18 DOI: 10.1016/j.molp.2024.12.010

Kai Jiang, Birger Lindberg Møller, Shaofan Luo, Yu Yang, David R Nelson, Elizabeth Heather Jakobsen Neilson, Joachim Møller Christensen, Kai Hua, Chao Hu, Xinhua Zeng, Mohammed Saddik Motawie, Tao Wan, Guang-Wan Hu, Guy Eric Onjalalaina, Yijiao Wang, Juan Diego Gaitán-Espitia, Zhiwen Wang, Xiao-Yan Xu, Jiamin He, Linying Wang, Yuanyuan Li, Dong-Hui Peng, Siren Lan, Huiming Zhang, Qing-Feng Wang, Zhong-Jian Liu, Wei-Chang Huang

{"title":"Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid.","authors":"Kai Jiang, Birger Lindberg Møller, Shaofan Luo, Yu Yang, David R Nelson, Elizabeth Heather Jakobsen Neilson, Joachim Møller Christensen, Kai Hua, Chao Hu, Xinhua Zeng, Mohammed Saddik Motawie, Tao Wan, Guang-Wan Hu, Guy Eric Onjalalaina, Yijiao Wang, Juan Diego Gaitán-Espitia, Zhiwen Wang, Xiao-Yan Xu, Jiamin He, Linying Wang, Yuanyuan Li, Dong-Hui Peng, Siren Lan, Huiming Zhang, Qing-Feng Wang, Zhong-Jian Liu, Wei-Chang Huang","doi":"10.1016/j.molp.2024.12.010","DOIUrl":"10.1016/j.molp.2024.12.010","url":null,"abstract":"Angraecum sesquipedale, also known as Darwin's orchid, possesses an exceptionally long nectar spur. Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis, later identified as Xanthopan praedicta. In this plant-pollinator interaction, the A. sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes (R1R2C = N-OH) to attract crepuscular and nocturnal pollinators. The molecular mechanism of oxime biosynthesis remains unclear in orchids. Here, we present the chromosome-level genome of A. sesquipedale. The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes. Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A. sesquipedale genome nor the genomes of other members of the orchid family. Metabolomic analysis of the A. sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage. By integrating metabolomic and transcriptomic correlation approaches, flavin-containing monooxygenases (FMOs) encoded by six tandem-repeat genes in the A. sesquipedale genome are identified as catalyzing the formation of oximes present. Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis. We designate these FMOs as orchid oxime synthases 1-6. The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin's orchid provide new insights into the convergent evolution of biosynthetic pathways.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"392-415"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864900","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}

引用次数: 0

Chloroplast state transitions modulate nuclear genome stability via cytokinin signaling in Arabidopsis.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-28 DOI: 10.1016/j.molp.2025.01.021

Yajun Zeng, Sujuan Duan, Yawen Wang, Zhifeng Zheng, Zeyi Wu, Meihui Shi, Manchun Wang, Lan Jiang, Xue Li, Hong-Bin Wang, Hong-Lei Jin

{"title":"Chloroplast state transitions modulate nuclear genome stability via cytokinin signaling in Arabidopsis.","authors":"Yajun Zeng, Sujuan Duan, Yawen Wang, Zhifeng Zheng, Zeyi Wu, Meihui Shi, Manchun Wang, Lan Jiang, Xue Li, Hong-Bin Wang, Hong-Lei Jin","doi":"10.1016/j.molp.2025.01.021","DOIUrl":"10.1016/j.molp.2025.01.021","url":null,"abstract":"Activities of the chloroplasts and nucleus are coordinated by retrograde signaling, which play crucial roles in plant development and environmental adaptation. However, the connection between chloroplast status and nuclear genome stability is poorly understood. Chloroplast state transitions enable the plant to balance photosystem absorption capacity in an environment with changing light quality. Here, we report that abnormal chloroplast state transitions lead to instability in the nuclear genome and impaired plant growth. We observed increased DNA damage in the state transition-defective Arabidopsis thaliana mutant stn7, and demonstrated that this damage was triggered by cytokinin accumulation and activation of cytokinin signaling. We showed that cytokinin signaling promotes a competitive association between ARABIDOPSIS RESPONSE REGULATOR 10 (ARR10) with PROLIFERATING CELLULAR NUCLEAR ANTIGEN 1/2 (PCNA1/2), inhibiting the binding of PCNA1/2 to nuclear DNA. This affects DNA replication, leading to replication-dependent genome instability. Treatment with 2,5-dibromo-3-methyl-6-isopropylbenzoquinone that simulates the reduction of the plastoquinone pool during abnormal state transitions increased the accumulation of ARABIDOPSIS HISTIDINE-CONTAINING PHOSPHOTRANSMITTER 1, a phosphotransfer protein involved in cytokinin signaling, and promoted the interaction between ARR10 with PCNA1/2, leading to increased DNA damage. These findings highlight the function of cytokinin signaling in coordinating chloroplast function and nuclear genome integrity during plant acclimation to environmental changes.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"513-526"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066843","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}

引用次数: 0

New molecular chaperone roles for CO₂ assimilation in early land plants. 早期陆生植物CO2同化的新分子伴侣作用。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-19 DOI: 10.1016/j.molp.2025.01.015

Julie L McDonald, Robert H Wilson

引用次数: 0

Sculpting the growth-defense trade-off by H₂S.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-30 DOI: 10.1016/j.molp.2025.01.023

Hongfei Li, Yanjie Xie

引用次数: 0

A small RNA effector conserved in herbivore insects suppresses host plant defense by cross-kingdom gene silencing. 在食草昆虫中保守的小RNA效应物通过跨界基因沉默抑制寄主植物防御。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-03 DOI: 10.1016/j.molp.2025.01.001

Wen-Hao Han, Shun-Xia Ji, Feng-Bin Zhang, Hong-Da Song, Jun-Xia Wang, Xiao-Ping Fan, Rui Xie, Shu-Sheng Liu, Xiao-Wei Wang

{"title":"A small RNA effector conserved in herbivore insects suppresses host plant defense by cross-kingdom gene silencing.","authors":"Wen-Hao Han, Shun-Xia Ji, Feng-Bin Zhang, Hong-Da Song, Jun-Xia Wang, Xiao-Ping Fan, Rui Xie, Shu-Sheng Liu, Xiao-Wei Wang","doi":"10.1016/j.molp.2025.01.001","DOIUrl":"10.1016/j.molp.2025.01.001","url":null,"abstract":"Herbivore insects deploy salivary effectors to manipulate the defense of their host plants. However, it remains unclear whether small RNAs from insects can function as effectors in regulating plant-insect interactions. Here, we report that a microRNA (miR29-b) found in the saliva of the phloem-feeding whitefly (Bemisia tabaci) can transfer into the host plant phloem during feeding and fine-tune the defense response of tobacco (Nicotiana tabacum) plants. We show that the salivary gland-enriched BtmiR29-b is produced by BtDicer 1 and released into tobacco cells via salivary exosomes. Once inside the plant cells, BtmiR29-b hijacks tobacco Argonaute 1 to silence the defense gene Bcl-2-associated athanogene 4 (NtBAG4). In tobacco, NtBAG4 acts as the positive regulator of phytohormones salicylic acid (SA) and jasmonic acid (JA), enhancing plant defense against whitefly attacks. Interestingly, we also found that miR29-b acts as a salivary effector in another Hemipteran insect, the aphid Myzus persicae, which inhibits tobacco resistance by degrading NtBAG4. Moreover, miR29-b is highly conserved in Hemiptera and across other insect orders such as Coleoptera, Hymenoptera, Orthoptera, and Blattaria. Computational analysis suggests that miR29-b may also target the evolutionarily conserved BAG4 gene in other plant species. We further provide evidence showing BtmiR29-b-mediated BAG4 cleavage and defense suppression in tomato (Solanum lycopersicum). Taken together, our work reveals that a conserved miR29-b effector from insects fine-tunes plant SA- and JA-mediated defense by cross-kingdom silencing of the host plant BAG4 gene, providing new insight into the defense and counter-defense mechanisms between herbivores and their host plants.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"437-456"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927648","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}

引用次数: 0

NTRC's novel role: Bridging chloroplast redox oscillations and nuclear circadian clock.

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 DOI: 10.1016/j.molp.2025.03.003

Francisco Javier Cejudo

引用次数: 0

Getting the SCOOP on peptide ligands that regulate leaf senescence. 获得关于调节叶片衰老的肽配体的独家信息。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-16 DOI: 10.1016/j.molp.2025.01.013

Judy A Brusslan

引用次数: 0