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Huang Y, Yang J, Sun X, Li J, Cao X, Yao S, Han Y, Chen C, Du L, Li S, Ji Y, Zhou T, Wang H, Han JJ, Wang W, Wei C, Xie Q, Yang Z, Li Y. Perception of viral infections and initiation of antiviral defence in rice. Nature 2025; 641:173-181. [PMID: 40074903 PMCID: PMC12043510 DOI: 10.1038/s41586-025-08706-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/27/2025] [Indexed: 03/14/2025]
Abstract
Crop production faces persistent threats from insect-vector-borne viral diseases1,2. Recent advancements have revealed the intricate immune mechanisms that plants deploy against viral pathogens3-8. However, the molecular mechanisms through which plant hosts recognize viral infections and initiate antiviral defence at disease onset have not been elucidated. Here, through the natural infection of rice by inoculation with insect vectors carrying the natural forms of viruses, we show that viral coat proteins are perceived by the RING1-IBR-RING2-type ubiquitin ligase (RBRL), initiating the first step of the natural antiviral response in rice. RBRL subsequently targets an adaptor protein of the transcriptional repression complex of the jasmonate pathway, NOVEL INTERACTOR OF JAZ 3 (NINJA3), for degradation through the ubiquitination system, inducing jasmonate signalling and activating downstream antiviral defence. We further show that this phenomenon is a universal molecular mechanism used by rice plants to perceive viral infections and initiate antiviral signalling cascades. This approach is important not only for obtaining a deeper understanding of virus-host interactions but also for further disease resistance breeding.
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Affiliation(s)
- Yu Huang
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, P. R. China
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, P. R. China
| | - Jialin Yang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P. R. China
- State Key Laboratory of Agricultural and Forestry Biosecurity, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Xi Sun
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, P. R. China
- State Key Laboratory of Agricultural and Forestry Biosecurity, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Jiahao Li
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, P. R. China
- State Key Laboratory of Agricultural and Forestry Biosecurity, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Xiaoqiang Cao
- Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Shengze Yao
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, P. R. China
| | - Yanhong Han
- State Key Laboratory of Agricultural and Forestry Biosecurity, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Changtian Chen
- State Key Laboratory of Agricultural and Forestry Biosecurity, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Shuo Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Yinghua Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, P. R. China
| | - Jia-Jia Han
- Institute of Biodiversity, School of Ecology and Environmental Science Yunnan University, Kunming, P. R. China
| | - Wenming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, P. R. China
| | - Chunhong Wei
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, P. R. China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- National Center of Technology Innovation for Maize, State Key Laboratory of Crop Germplasm Innovation and Molecular Breeding, Syngenta Group China, Beijing, P. R. China
| | - Zhirui Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, P. R. China.
| | - Yi Li
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, P. R. China.
- State Key Laboratory of Agricultural and Forestry Biosecurity, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, P. R. China.
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Thyssen GN, Smith W, Naoumkina M, Pinnika G, Jenkins JN, McCarty JC, Li P, Florane CB, Jones DC, Fang DD. Allele and transcriptome mining in Gossypium hirsutum reveals variation in candidate genes at genetic loci affecting cotton fiber quality and textile flammability. BMC PLANT BIOLOGY 2025; 25:305. [PMID: 40059154 PMCID: PMC11892310 DOI: 10.1186/s12870-025-06306-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 02/25/2025] [Indexed: 05/13/2025]
Abstract
BACKGROUND Breeding valuable traits in crop plants requires identifying diverse alleles in the germplasm that are likely to affect desirable characteristics. The genetic diversity of historic cultivars of cotton is a reservoir of potentially important genes for crop improvement and genetic research. Diversity in the characteristics of harvested cotton fibers affects their suitability for end-use applications. Candidate loci and genes have been identified that affect the length, strength, and maturity of cotton fibers which affect the quality and value of the yarn, thread and textile. Natural genetic mechanisms in the plant may also affect the flammability of the produced textiles. RESULTS Here we show that a combination of allele mining and transcriptome analysis can identify candidate genes for cotton fiber traits including strength and perhaps flammability. We found novel DNA variants in fiber-expressed gene families in 132 newly sequenced cotton varieties and identified genes with genotype-specific RNA expression. CONCLUSIONS Among these, we identified novel variation in DNA sequence and RNA expression in genes at major QTL qD04-ELO-WLIM (JGI-Gohir.D04G160000), qA13-MIC (Gohir.A13G157500), qA07-STR (Gohir.A07G191600), supported the candidacy of qD11-UHML-KRP6 (Gohir.D11G197900) and qD13-STR (Gohir.D13G17450), and identified an additional A03-WLIM transcription factor gene (Gohir.A03G182100) and several RNA expression variant candidates of potential flammability genes that may be useful for plant biologists and cotton breeders. Candidate genes for traits like flame resistance that are likely due to the combination of many small effect QTL can benefit from this multi-mining approach. We provide an annotated variant call format (vcf) file with variations at 24,996 loci that are predicted to affect 10,418 cotton fiber genes in the historic breeding germplasm.
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Affiliation(s)
- Gregory N Thyssen
- Cotton Fiber Bioscience & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA.
| | - Wayne Smith
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Marina Naoumkina
- Cotton Fiber Bioscience & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Ganesh Pinnika
- Cotton Fiber Bioscience & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, USA
| | - Jack C McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, USA
| | - Ping Li
- Cotton Fiber Bioscience & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Christopher B Florane
- Cotton Fiber Bioscience & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | | | - David D Fang
- Cotton Fiber Bioscience & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
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Rab SO, Zwamel AH, Oghenemaro EF, Chandra M, Kaur I, Rani B, Abbot V, Kumar MR, Ullah MI, Kumar A. Cell death-associated lncRNAs in cancer immunopathogenesis: An exploration of molecular mechanisms and signaling pathways. Exp Cell Res 2025; 446:114439. [PMID: 39947388 DOI: 10.1016/j.yexcr.2025.114439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 12/07/2024] [Accepted: 02/10/2025] [Indexed: 02/19/2025]
Abstract
Cancer remains one of the foremost causes of mortality worldwide, highlighting the urgent need for novel therapeutic targets due to the insufficient efficacy and adverse side effects associated with existing cancer treatments. Long non-coding RNAs (lncRNAs), defined as RNA transcripts longer than 200 nucleotides, have emerged as pivotal regulators in the initiation and progression of various malignancies. In oncology, programmed cell death (PCD) serves as the primary mechanism for tumor cell elimination, comprising processes such as apoptosis, pyroptosis, autophagy, and ferroptosis. Recent studies have elucidated a substantial relationship between lncRNAs and these PCD pathways, indicating that lncRNAs can modulate the apoptotic and non-apoptotic death mechanisms. This regulation may influence not only the dynamics of cancer progression but also the therapeutic response to clinical interventions. This review delves into the intricate role of lncRNAs within the context of PCD in cancer, unveiling the underlying pathogenic mechanisms while proposing innovative strategies for cancer therapy. Additionally, it discusses the potential therapeutic implications of targeting lncRNAs in PCD and related signaling pathways, aiming to enhance treatment outcomes for patients facing cancer.
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Affiliation(s)
- Safia Obaidur Rab
- Central Labs, King Khalid University, AlQura'a, P.O. Box 960, Abha, Saudi Arabia; Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Ahmed Hussein Zwamel
- Medical Laboratory Technique College, The Islamic University, Najaf, Iraq; Medical Laboratory Technique College, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; Medical Laboratory Technique College, The Islamic University of Babylon, Babylon, Iraq
| | - Enwa Felix Oghenemaro
- Delta State University, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, PMB 1 Abraka, Delta State, Nigeria
| | - Muktesh Chandra
- Marwadi University Research Center, Department of Bioinformatics, Faculty of Engineering and Technology, Marwadi University, Rajkot, 360003, Gujarat, India
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka, 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India.
| | - Bindu Rani
- Department of Medicine, National Institute of Medical Sciences, NIMS University Rajasthan, Jaipur, India
| | - Vikrant Abbot
- Chandigarh Pharmacy College, Chandigarh Group of Colleges-Jhanjeri, Mohali, 140307, Punjab, India
| | - M Ravi Kumar
- Department of Basic Science & Humanities, Raghu Engineering College, Visakhapatnam, India
| | - Muhammad Ikram Ullah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72388, Aljouf, Saudi Arabia
| | - Abhinav Kumar
- Department of Nuclear and Renewable Energy, Ural Federal University Named After the First President of Russia Boris Yeltsin, Ekaterinburg, 620002, Russia; Department of Mechanical Engineering, Karpagam Academy of Higher Education, Coimbatore, 641021, India
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4
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Yi X, Hussain I, Zhang P, Xiao C. Nuclear-Targeting Peptides for Cancer Therapy. Chembiochem 2024; 25:e202400596. [PMID: 39215136 DOI: 10.1002/cbic.202400596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/19/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
Nucleus is the central regulator of cells that controls cell proliferation, metabolism, and cell cycle, and is considered the most important organelle in cells. The precision medicine that can achieve nuclear targeting has achieved good therapeutic effects in anti-tumor therapy. However, the presence of biological barriers such as cell membranes and nuclear membranes in cells limit the delivery of therapeutic agents to the nucleus. Therefore, developing effective nuclear-targeting drug delivery strategies is particularly important. Nuclear-targeting peptides are a class of functional peptides that can penetrate cell membranes and target the nucleus. They mainly recognize and bind to the nuclear transport molecules (such as Importin-α/β) and transport the therapeutic agents to the nucleus through nuclear pore complexes (NPC). This review summarizes the most recent developments of strategies for anti-tumor therapy utilizing nuclear-targeting peptides, which will ultimately contribute to the development of more effective nuclear-targeting strategies to achieve better anti-tumor outcomes.
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Affiliation(s)
- Xuan Yi
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China
| | - Irshad Hussain
- Department of Chemistry and Chemical Engineering, SBA School of Science & Engineering, Lahore University of Management Sciences (LUMS). DHA, Lahore, 54792, Pakistan
| | - Peng Zhang
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China
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El Arbi N, Nardeli SM, Šimura J, Ljung K, Schmid M. The Arabidopsis splicing factor PORCUPINE/SmE1 orchestrates temperature-dependent root development via auxin homeostasis maintenance. THE NEW PHYTOLOGIST 2024; 244:1408-1421. [PMID: 39327913 DOI: 10.1111/nph.20153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 08/24/2024] [Indexed: 09/28/2024]
Abstract
Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.
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Affiliation(s)
- Nabila El Arbi
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Sarah Muniz Nardeli
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, S-75007, Uppsala, Sweden
| | - Jan Šimura
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Markus Schmid
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, S-75007, Uppsala, Sweden
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Wang Z, Zhang X, Liu C, Duncan S, Hang R, Sun J, Luo L, Ding Y, Cao X. AtPRMT3-RPS2B promotes ribosome biogenesis and coordinates growth and cold adaptation trade-off. Nat Commun 2024; 15:8693. [PMID: 39375381 PMCID: PMC11488217 DOI: 10.1038/s41467-024-52945-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 09/25/2024] [Indexed: 10/09/2024] Open
Abstract
Translation, a fundamental process regulating cellular growth and proliferation, relies on functional ribosomes. As sessile organisms, plants have evolved adaptive strategies to maintain a delicate balance between growth and stress response. But the underlying mechanisms, particularly on the translational level, remain less understood. In this study, we revealed the mechanisms of AtPRMT3-RPS2B in orchestrating ribosome assembly and managing translational regulation. Through a forward genetic screen, we identified PDCD2-D1 as a suppressor gene restoring abnormal development and ribosome biogenesis in atprmt3-2 mutants. Our findings confirmed that PDCD2 interacts with AtPRMT3-RPS2B, and facilitates pre-ribosome transport through nuclear pore complex, finally ensuring normal ribosome translation in the cytoplasm. Additionally, the dysfunction of AtPRMT3-RPS2B was found to enhance freezing tolerance. Moreover, we revealed that AtPRMT3-RPS2B promotes the translation of housekeeping mRNAs while concurrently repressing stress-related mRNAs. In summary, our study sheds light on the regulatory roles of AtPRMT3-RPS2B in ribosome assembly and translational balance, enabling the trade-off between growth and stress.
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Affiliation(s)
- Zhen Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
| | - Xiaofan Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunyan Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Susan Duncan
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Runlai Hang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jing Sun
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lilan Luo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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7
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Muñoz-Díaz E, Fuenzalida-Valdivia I, Darrière T, de Bures A, Blanco-Herrera F, Rompais M, Carapito C, Sáez-Vásquez J. Proteomic profiling of Arabidopsis nuclei reveals distinct protein accumulation kinetics upon heat stress. Sci Rep 2024; 14:18914. [PMID: 39143125 PMCID: PMC11324732 DOI: 10.1038/s41598-024-65558-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/20/2024] [Indexed: 08/16/2024] Open
Abstract
Heat stress (HS) impacts the nuclear proteome and, subsequently, protein activities in different nuclear compartments. In Arabidopsis thaliana, a short exposure to 37 °C leads to loss of the standard tripartite architecture of the nucleolus, the most prominent nuclear substructure, and, consequently, affects the assembly of ribosomes. Here, we report a quantitative label-free LC‒MS/MS (Liquid Chromatography coupled to tandem Mass Spectrometry) analysis to determine the nuclear proteome of Arabidopsis at 22 °C, HS (37 °C for 4 and 24 h), and a recovery phase. This analysis identified ten distinct groups of proteins based on relative abundance changes in the nucleus before, during and after HS: Early, Late, Transient, Early Persistent, Late Persistent, Recovery, Early-Like, Late-Like, Transient-Like and Continuous Groups (EG, LG, TG, EPG, LPG, RG, ELG, LLG, TLG and CG, respectively). Interestingly, the RNA polymerase I subunit NRPA3 and other main nucleolar proteins, including NUCLEOLIN 1 and FIBRILLARIN 1 and 2, were detected in RG and CG, suggesting that plants require increased nucleolar activity and likely ribosome assembly to restore protein synthesis after HS.
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Affiliation(s)
- E Muñoz-Díaz
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860, Perpignan, France
- LGDP, UMR 5096, Univ. Perpignan Via Domitia, 66860, Perpignan, France
| | - I Fuenzalida-Valdivia
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, 8370146, Santiago, RM, Chile
- ANID - Millennium Institute for Integrative Biology (IBio), Santiago, Chile
- ANID - Millennium Science Initiative Program, Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), 8331150, Santiago, Chile
| | - T Darrière
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860, Perpignan, France
- LGDP, UMR 5096, Univ. Perpignan Via Domitia, 66860, Perpignan, France
| | - A de Bures
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860, Perpignan, France
- LGDP, UMR 5096, Univ. Perpignan Via Domitia, 66860, Perpignan, France
| | - F Blanco-Herrera
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andrés Bello, 8370146, Santiago, RM, Chile
- ANID - Millennium Institute for Integrative Biology (IBio), Santiago, Chile
- ANID - Millennium Science Initiative Program, Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), 8331150, Santiago, Chile
| | - M Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - C Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - J Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860, Perpignan, France.
- LGDP, UMR 5096, Univ. Perpignan Via Domitia, 66860, Perpignan, France.
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8
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Ranty-Roby S, Pontvianne F, Quentin M, Favery B. The overlooked manipulation of nucleolar functions by plant pathogen effectors. FRONTIERS IN PLANT SCIENCE 2024; 15:1445097. [PMID: 39175483 PMCID: PMC11339880 DOI: 10.3389/fpls.2024.1445097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 07/16/2024] [Indexed: 08/24/2024]
Abstract
Pathogens need to manipulate plant functions to facilitate the invasion of their hosts. They do this by secreting a cocktail of molecules called effectors. Studies of these molecules have mostly focused on the mechanisms underlying their recognition and the subsequent transcriptional reprogramming of cells, particularly in the case of R gene-dependent resistance. However, the roles of these effectors are complex, as they target all cell compartments and their plant targets remain largely uncharacterized. An understanding of the mechanisms involved would be a considerable asset for plant breeding. The nucleolus is the site of many key cellular functions, such as ribosome biogenesis, cellular stress regulation and many other functions that could be targets for pathogenicity. However, little attention has been paid to effectors targeting nucleolar functions. In this review, we aim to fill this gap by providing recent findings on pathogen effectors that target and manipulate nucleolar functions and dynamics to promote infection. In particular, we look at how some effectors hijack ribosome biogenesis, the modulation of transcription or alternative splicing, all key functions occurring at least partially in the nucleolus. By shedding light on the role of the plant nucleolus in pathogen interactions, this review highlights the importance of understanding nucleolar biology in the context of plant immunity and the mechanisms manipulated by plant pathogens.
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Affiliation(s)
- Sarah Ranty-Roby
- INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis F-06903, Sophia Antipolis, France
| | | | - Michaël Quentin
- INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis F-06903, Sophia Antipolis, France
| | - Bruno Favery
- INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech (ISA), Sophia Antipolis F-06903, Sophia Antipolis, France
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
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9
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Skowicki M, Tarvirdipour S, Kraus M, Schoenenberger CA, Palivan CG. Nanoassemblies designed for efficient nuclear targeting. Adv Drug Deliv Rev 2024; 211:115354. [PMID: 38857762 DOI: 10.1016/j.addr.2024.115354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
One of the key aspects of coping efficiently with complex pathological conditions is delivering the desired therapeutic compounds with precision in both space and time. Therefore, the focus on nuclear-targeted delivery systems has emerged as a promising strategy with high potential, particularly in gene therapy and cancer treatment. Here, we explore the design of supramolecular nanoassemblies as vehicles to deliver specific compounds to the nucleus, with the special focus on polymer and peptide-based carriers that expose nuclear localization signals. Such nanoassemblies aim at maximizing the concentration of genetic and therapeutic agents within the nucleus, thereby optimizing treatment outcomes while minimizing off-target effects. A complex scenario of conditions, including cellular uptake, endosomal escape, and nuclear translocation, requires fine tuning of the nanocarriers' properties. First, we introduce the principles of nuclear import and the role of nuclear pore complexes that reveal strategies for targeting nanosystems to the nucleus. Then, we provide an overview of cargoes that rely on nuclear localization for optimal activity as their integrity and accumulation are crucial parameters to consider when designing a suitable delivery system. Considering that they are in their early stages of research, we present various cargo-loaded peptide- and polymer nanoassemblies that promote nuclear targeting, emphasizing their potential to enhance therapeutic response. Finally, we briefly discuss further advancements for more precise and effective nuclear delivery.
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Affiliation(s)
- Michal Skowicki
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Manuel Kraus
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
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Serafini-Fracassini D, Del Duca S. Programmed Cell Death Reversal: Polyamines, Effectors of the U-Turn from the Program of Death in Helianthus tuberosus L. Int J Mol Sci 2024; 25:5386. [PMID: 38791426 PMCID: PMC11121942 DOI: 10.3390/ijms25105386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/22/2024] [Accepted: 04/08/2024] [Indexed: 05/26/2024] Open
Abstract
This review describes a 50-year-long research study on the characteristics of Helianthus tuberosus L. tuber dormancy, its natural release and programmed cell death (PCD), as well as on the ability to change the PCD so as to return the tuber to a life program. The experimentation on the tuber over the years is due to its particular properties of being naturally deficient in polyamines (PAs) during dormancy and of immediately reacting to transplants by growing and synthesizing PAs. This review summarizes the research conducted in a unicum body. As in nature, the tuber tissue has to furnish its storage substances to grow vegetative buds, whereby its destiny is PCD. The review's main objective concerns data on PCD, the link with free and conjugated PAs and their capacity to switch the destiny of the tuber from a program of death to one of new life. PCD reversibility is an important biological challenge that is verified here but not reported in other experimental models. Important aspects of PA features are their capacity to change the cell functions from storage to meristematic ones and their involvement in amitosis and differentiation. Other roles reported here have also been confirmed in other plants. PAs exert multiple diverse roles, suggesting that they are not simply growth substances, as also further described in other plants.
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Affiliation(s)
| | - Stefano Del Duca
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
- Interdepartmental Centre for Agri-Food Industrial Research, University of Bologna, 40126 Bologna, Italy
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11
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Ando S, Nomoto M, Iwakawa H, Vial-Pradel S, Luo L, Sasabe M, Ohbayashi I, Yamamoto KT, Tada Y, Sugiyama M, Machida Y, Kojima S, Machida C. Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3621. [PMID: 37896084 PMCID: PMC10610122 DOI: 10.3390/plants12203621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants.
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Affiliation(s)
- Sayuri Ando
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Simon Vial-Pradel
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Michiko Sasabe
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho, Hirosaki 036-8561, Japan;
| | - Iwai Ohbayashi
- Department of Life Sciences, National Cheng Kung University, Tainan City 701, Taiwan;
| | - Kotaro T. Yamamoto
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Munetaka Sugiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Yasunori Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
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12
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Taliansky ME, Love AJ, Kołowerzo-Lubnau A, Smoliński DJ. Cajal bodies: Evolutionarily conserved nuclear biomolecular condensates with properties unique to plants. THE PLANT CELL 2023; 35:3214-3235. [PMID: 37202374 PMCID: PMC10473218 DOI: 10.1093/plcell/koad140] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/20/2023]
Abstract
Proper orchestration of the thousands of biochemical processes that are essential to the life of every cell requires highly organized cellular compartmentalization of dedicated microenvironments. There are 2 ways to create this intracellular segregation to optimize cellular function. One way is to create specific organelles, enclosed spaces bounded by lipid membranes that regulate macromolecular flux in and out of the compartment. A second way is via membraneless biomolecular condensates that form due to to liquid-liquid phase separation. Although research on these membraneless condensates has historically been performed using animal and fungal systems, recent studies have explored basic principles governing the assembly, properties, and functions of membraneless compartments in plants. In this review, we discuss how phase separation is involved in a variety of key processes occurring in Cajal bodies (CBs), a type of biomolecular condensate found in nuclei. These processes include RNA metabolism, formation of ribonucleoproteins involved in transcription, RNA splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles of CBs, we discuss unique plant-specific functions of CBs in RNA-based regulatory pathways such as nonsense-mediated mRNA decay, mRNA retention, and RNA silencing. Finally, we summarize recent progress and discuss the functions of CBs in responses to pathogen attacks and abiotic stresses, responses that may be regulated via mechanisms governed by polyADP-ribosylation. Thus, plant CBs are emerging as highly complex and multifunctional biomolecular condensates that are involved in a surprisingly diverse range of molecular mechanisms that we are just beginning to appreciate.
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Affiliation(s)
| | - Andrew J Love
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Agnieszka Kołowerzo-Lubnau
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
| | - Dariusz Jan Smoliński
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
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13
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Durut N, Kornienko AE, Schmidt HA, Lettner N, Donà M, Nordborg M, Mittelsten Scheid O. Long noncoding RNAs contribute to DNA damage resistance in Arabidopsis thaliana. Genetics 2023; 225:iyad135. [PMID: 37467473 PMCID: PMC10471225 DOI: 10.1093/genetics/iyad135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023] Open
Abstract
Efficient repair of DNA lesions is essential for the faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant, and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged young Arabidopsis thaliana plants with two different types of genotoxic stress and performed de novo assembly and transcriptome analysis. We identified three long noncoding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. We generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in the Brassicaceae group. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for mechanistic analysis of their role.
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Affiliation(s)
- Nathalie Durut
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Aleksandra E Kornienko
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr Gasse 9, 1030 Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Mattia Donà
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
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14
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Dahmani I, Qin K, Zhang Y, Fernie AR. The formation and function of plant metabolons. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1080-1092. [PMID: 36906885 DOI: 10.1111/tpj.16179] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/26/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
Metabolons are temporary structural-functional complexes of sequential enzymes of a metabolic pathway that are distinct from stable multi-enzyme complexes. Here we provide a brief history of the study of enzyme-enzyme assemblies with a particular focus on those that mediate substrate channeling in plants. Large numbers of protein complexes have been proposed for both primary and secondary metabolic pathways in plants. However, to date only four substrate channels have been demonstrated. We provide an overview of current knowledge concerning these four metabolons and explain the methodologies that are currently being applied to unravel their functions. Although the assembly of metabolons has been documented to arise through diverse mechanisms, the physical interaction within the characterized plant metabolons all appear to be driven by interaction with structural elements of the cell. We therefore pose the question as to what methodologies could be brought to bear to enhance our knowledge of plant metabolons that assemble via different mechanisms? In addressing this question, we review recent findings in non-plant systems concerning liquid droplet phase separation and enzyme chemotaxis and propose strategies via which such metabolons could be identified in plants. We additionally discuss the possibilities that could be opened up by novel approaches based on: (i) subcellular-level mass spectral imaging, (ii) proteomics, and (iii) emergent methods in structural and computational biology.
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Affiliation(s)
- Ismail Dahmani
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Kezhen Qin
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
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