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Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants

Molecular Plant 2024年第3期17卷 377-394页

作者： Paolo M.Triozzi Luca Brunello Giacomo Novi Gianmarco Ferri Francesco Cardarelli Elena Loreti Mariano Perales Pierdomenico Perata PlantLab Center of Plant SciencesSant'Anna School of Advanced Studies56010 PisaItaly centro de biotecnologia y genomica de plantas Universidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA-CSIC)Campus de Montegancedo UPMPozuelo de Alarcon28223 MadridSpain Fondazione Pisana per la Scienza 56017 PisaItaly Laboratorio NEST Scuola Normale SuperioreIstituto Nanoscienze-CNRPiazza S.Silvestro1256127 PisaItaly institute of Agricultural Biology and Biotechnology National Research Council56124 PisaItaly departamento de biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUniversidad Politecnica de Madrid(UPM)28040 Madrid.Spain

Oxygen is essential for plant growth and *** occurs in plants due to limited oxygen avail-abilityfollowing adverse environmental conditions as well inhypoxic niches in otherwisenormoxic ***,the existence and functional integration of spatiotemporal oxygen dynamics with plant development remains *** animal systems dynamic fluctuations in oxygen availability are known as cyclic *** this study,we demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of Arabidopsis *** hypoxia in plants is based on a mechanism requiring the ETHyLENE RESPONSE FACTORS type VII(ERFVII)that are central components of the oxygen-sensing machinery in *** ERFVll-dependent mechanism allows precise adjustment of leaf growth in response to carbon status and oxygen availability within plant *** study thus establishes a functional connection between internal spatiotemporal oxygen dynamics and developmental processes of plants.

关键词： Arabidopsis hypoxia cyclic hypoxia leaf development oxygen-sensing mechanism ERFVII

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Building Expertise on FAIR Through Evolving Bring your Own Data(ByOD) Workshops: describing the Data, Software, and Management-focused Approaches and Their Evolution

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Data Intelligence 2024年第2期6卷 429-456页

作者： César H.Bernabé Lieze Thielemans Rajaram Kaliyaperumal Claudio Carta Shuxin Zhang Celia W.G.van Gelder Nirupama Benis Luiz Olavo Bonino da Silva Santos Ronald Cornet Bruna dos Santos Vieira Nawel Lalout Ines Henriques Alberto Camara Ballesteros Kees Burger Martijn G.Kersloot Friederike Ehrhart Esther van Enckevort Chris T.Evelo Alasdair J.G.Gray Marc Hanauer Kristina Hettne Joep de Ligt Arnaldo Pereira Nuria Queralt-Rosinach Erik Schultes Domenica Taruscio Andra Waagmeester Mark D.Wilkinson Egon L.Willighagen Mascha Jansen Barend Mons Marco Roos Annika Jacobsen Biosemantics Group Department of Human GeneticsLeiden University Medical CentreLeidenThe Netherlands NIHR Academic Fellow in General Practice University College London and The Royal Free NHS Foundation Trust National Centre for Rare Diseases Istituto Superiore di SanitaRomeItaly department of Medical Informatics Amsterdam UMC location University of AmsterdamMeibergdreef 9AmsterdamThe Netherlands Amsterdam Public Health Methodology&Digital HealthAmsterdamThe Netherlands Health-Rl UtrechtThe Netherlands Semantics Services and Cybersecurity groupUniversity of TwenteEnschedeThe Netherlands department of Medical Imaging Radboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands department of Medical BioSciences Radboud University Medical CenterNijmegenThe Netherlands The Duchenne Parent Project VeneendaalThe Netherlands departamento de biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de PlantasUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC(INIA-CSIC).Campus MontegancedoPozuelo de Alarcon(Madrid)Spain Castor AmsterdamThe Netherlands department of Bioinformatics-BiGCaT Maastricht UniversityMaastrichtThe Netherlands University Medical Center Groningen University of GroningenGroningenThe Netherlands Maastricht Centre for Systems Biology(MaCSBio) Maastricht UniversityMaastrichtThe Netherlands department of Computer Science Heriot-Watt UniversityEdinburghUK INSERM US14-OrphanetPlateforme Maladies RaresParisFrance Centre for Digital Scholarship Leiden University LibrariesThe Netherlands Center for Molecular Medicine Cancer Genomics NetherlandsDepartment of GeneticsUniversity Medical Center UtrechtUniversity UtrechtThe Netherlands University of Aveiro DETI/IEETAAveiroPortugal GO FAIR Foundation LeidenThe Netherlands The Leiden Academic Center for Drug Research LeidenThe Netherlands Micel

Since 2014,"Bring your Own Data"workshops(ByODs)have been organised to inform people about the process and benefits of making resources Findable,Accessible,Interoperable,and Reusable(FAIR,and the FAIRification process).The ByOD workshops'content and format differ depending on their goal,context,and the background and needs of ***-focused ByODs educate domain experts on how to make their data FAIR to find new answers to research ***-focused ByODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification ***-focused ByODs gather software developers and experts on FAIR to implement or improve software resources that are used to support ***,these ByODs intend to foster collaboration between different types of stakeholders involved in data management,curation,and reuse(*** experts,trainers,developers,data owners,data analysts,FAIR experts).The ByODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and *** this paper,we detail the three different structures of the ByODs and describe examples of early ByODs related to plant breeding data,and rare disease registries and biobanks,which have shaped the structure of the *** discuss the latest insights into making ByODs more productive by leveraging our almost ten years of training experience in these workshops,including successes and encountered ***,we examine how the participants'feedback has motivated the research on FAIR,including the development of workflows and software.

关键词： FAIR FAIRification FAIR expertise Bring your Own Data Workshop ByOD

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OsDMI3,a Ca^(2+)/calmodulin kinase,integrates and amplifies H_(2)O_(2) and Ca^(2+) signaling in ABA-mediated responses

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Molecular Plant 2023年第6期16卷 968-970页

作者： Miguel-Angel Torres Diego Jose Berlanga centro de biotecnologia y genomica de plantas Universidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA/CSIC)Campus de Montegancedo UPM28223 Pozuelo de AlarconMadridSpain departamento de biotecnologia-Biologia Vegetal Escuela Técnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUPM28040 MadridSpain

Abscisic acid(ABA)is an important hormone that regulates both plant development and stress responses(Chen et al.,2020).In the absence of ABA,group A PROTEIN PHOSPHATASE 2Cs(PP2Cs)interact with and inhibit SUCROSE-NON-FERMENTING 1-RELATED KINASES 2(SnRK2s).When ABA is present,ABA receptor PyRABACTIN RESISTANCE 1 and PyRABACTIN RESISTANCE 1-LIKE PROTEINS bind to and inhibit PP2Cs,allowing phosphorylation and activation of SnRK2s that,in turn,phosphorylate downstream targets,such as transcription factors,ion channels,and transporters(Figure 1).

关键词： SnRK2 Figure

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The FAIR Data Point:Interfaces and Tooling

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Data Intelligence 2023年第1期5卷 184-201页

作者： Oussama Mohammed Benhamed Kees Burger Rajaram Kaliyaperumal Luiz Olavo Bonino da Silva Santos Marek Suchánek Jan Slifka Mark D.Wilkinsoni departamento de biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de Plantas UPM-INIAUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)MadridES 28223Spain Leiden University Medical Center Leiden2333 ZCthe Netherlands University of Twente Enschede7513 GBthe Netherlands Czech Technical University in Prague PragueCZ 15000Czech Republic

While the FAIR Principles do not specify a technical solution for'FAIRness',it was clear from the outset of the FAIR initiative that it would be useful to have commodity software and tooling that would simplify the creation of FAIR-compliant *** FAIR Data Point is a metadata repository that follows the DCAT(2)schema,and utilizes the Linked Data Platform to manage the hierarchical metadata layers as LDP *** has been a recent flurry of development activity around the FAIR Data Point that has significantly improved its power and *** we describe five specific tools—an installer,a loader,two Webbased interfaces,and an indexer-aimed at maximizing the uptake and utility of the FAIR Data Point.

关键词： FAIR Data Linked data Semantic Web Metadata User interfaces Tooling Semantic query

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FAIR Data Point:A FAIR-Oriented Approach for Metadata Publication

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Data Intelligence 2023年第1期5卷 163-183页

作者： Luiz Olavo Bonino da Silva Santos Kees Burger Rajaram Kaliyaperumal Mark D.Wilkinson Services and Cybersecurity group Faculty of Electrical EngineeringMathematics and Computer ScienceUniversity of Twente-Enschede7513GBthe Netherlands Biosemantics group Department of Human GeneticsLeiden University Medical Center-LeidenNL 2333 ZCthe Netherlands Escuela Técnica Superior de Ingenieria Agronomica Alimentaria y de BiosistemasCentro de Biotecnologia y Genomica de Plantas UPM-INIAUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)MadridES 28223Spain

Metadata,data about other digital objects,play an important role in FAIR with a direct relation to all FAIR *** this paper we present and discuss the FAIR Data Point(FDP),a software architecture aiming to define a common approach to publish semantically-rich and machine-actionable metadata according to the FAIR *** present the core components and features of the FDP,its approach to metadata provision,the criteria to evaluate whether an application adheres to the FDP specifications and the service to register,index and allow users to search for metadata content of available FDPs.

关键词： FAIR FAIR data point FAIR principles Metadata Interoperability Linked data Semantic interoperability

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Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores

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Journal of Integrative Plant Biology 2021年第2期63卷 312-326页

作者： M.Estrella Santamaria Alejandro Garcia Ana Amaiz Irene Rosa-Diaz Gara Romero-Hernandez Isabel Diaz Manuel Martinez centro de biotecnologia y genomica de plantas Instituto Nacional de Investigacion y Tecnologia Agraria y AlimentariaUniversidad Politecnica de MadridMadridSpain departamento de biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenierfa AgronomicaAlimentaria y de BiosistemasUniversidad Politecnica de MadridMadridSpain

Plants experience different abiotic/biotic stresses,which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonateinduced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.

关键词： Arabidopsis thaliana arthropod herbivore comparative transcriptomics plant defense Tetranychus urticae

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Prefoldins Negatively Regulate Cold Acclimation in Arabidopsis thaliana by Promoting Nuclear Proteasome-Mediated Hy5 degradation

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Molecular Plant 2017年第6期10卷 791-804页

作者： Carlos Perea-Resa Miguel A. Rodriguez-Milla Elisa Iniesto Vicente Rubio Julio Salinas departamento de Biologia Medioambiental Centro de Investigaciones Biologicas CSIC 28040 Madrid Spain departamento de Genetica Molecular de plantas Centro Nacional de Biotecnologia CSIC 28049 Madrid Spain present address: department of Molecular Biology Massachusetts General Hospital Boston MA 02214 USA present address: Unidad de biotecnologia Celular Instituto de Salud Garlos Ⅲ 28222 Madrid Spain

The process of cold acclimation is an important adaptive response whereby many plants from temperate regions increase their freezing tolerance after being exposed to low non-freezing temperatures. The correct development of this response relies on proper accumulation of a number of transcription factors that regulate expression patterns of cold-responsive genes. Multiple studies have revealed a variety of molecular mechanisms involved in promoting the accumulation of these transcription factors. Interestingly, however, the mechanisms implicated in controlling such accumulation to ensure their adequate levels remain largely unknown. In this work, we demonstrate that prefoldins （PFDs） control the levels of Hy5, an Arabidopsis transcription factor with a key role in cold acclimation by activating anthocyanin biosynthesis, in response to low temperature. Our results show that, under cold conditions, PFDs accumulate into the nucleus through a deLLA-dependent mechanism, where they interact with Hy5, triggering its ubiquitination and subsequent degradation. The degradation of Hy5 would result, in turn, in anthocyanin biosynthesis attenuation, ensuring the accurate development of cold acclimation. These findings uncover an unanticipated nuclear function for PFDs in plant responses to abiotic stresses.

关键词： prefoldins cold acclimation Arabidopsis Hy5 anthocyanin deLLAs

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Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue in itiation

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Molecular Plant 2021年第8期14卷 1362-1378页

作者： Laura Serrano-Ron Pablo Perez-Garcia Alvaro Sanchez-Corrionero Inmaculada Gude Javier Cabrera Pui-Leng Ip Kenneth D.Birnbaum Miguel A.Moreno-Risueno centro de biotecnologia y genomica de plantas Universidad Politecnica de Madrid(UPM)-lnstituto Naci on al de Investigacion y Tec no logia Agraria y Alimentaria(INIA)Pozuelo de Alarcon28223 MadridSpain departamento de biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUniversidad Politecnica de Madrid(UPM)28040 MadridSpain Center for Genomics and Systems Biology Department of BiologyNew York UniversityNew YorkNYUSA

Postembryonic organogenesis is critical for plant ***,lateral roots(LRs)form the bulk of mature root systems,yet the ontogeny of the LR primordium(LRP)is not *** this study,we performed the single-cell RNA sequencing through the first four stages of LR formation in *** analysis led to a model in which a single group of precursor cells,with a cell identity different from their pericycle origins,rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor *** ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary *** did not detect cells resembling epidermis or root cap,suggesting that outer tissues may form later,preceding LR *** this stage,some remaining initial precursor cells form the primordium flanks,while the rest create a reservoir of pluripotent cells that are able to replace the LR if *** ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a ***,our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells.

关键词： organogenesis patterning stem cells single-cell RNA-seq cell fate regeneration

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Regulation of the New Arabidopsis Imprinted Gene AtBMI1C Requires the Interplay of Different Epigenetic Mechanisms

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Molecular Plant 2012年第1期5卷 260-269页

作者： Fabian Bratzel Chaoyang Alexandra Angelova Gema Lopez-Torrejon Marcus Koch Juan Carlos del Pozo Myriam Calonje Centre for Organismal Studies Heidelberg Department of Biodiversity and Plant Systernatics University of Heidelberg Im Neuenheirner Feld 345 69120 Heidelberg Germany centro de biotecnologia y genomica de plantas （UPM-INIA） Campus de Montegancedo s/n Boadilla del Monte 28660 Madrid Spain

Recently, it has been shown that plants contain homologs to the animal Polycomb repressive complex I （PRC1） components BM11 and RINGIA/B. In Arabidopsis, there are three BMIl-like genes, two of which, AtBMIIA and B, are required during post-embryonic plant growth to repress embryonic traits and allow cell differentiation. However, little is known about the third BMIl-like gene, AtBMIIC. In this work, we show that AtBMIIC is only expressed during endosperm and stamen development. AtBMIIC is an imprinted gene expressed from the maternal allele in the endosperm but bialleli- cally expressed in stamen. We found that the characteristic expression pattern of AtBMIIC is the result of a complex epigenetic regulation that involves CG DNA methylation, RNA-directed non-CG DNA methylation （RdDM）, and PcG activity. Our results show the orchestrated interplay of different epigenetic mechanisms in regulating gene expression throughout development, shedding light on the current hypotheses for the origin and mechanism of imprinting in plant endosperm.

关键词： Epigenetics gene silencing development Polycomb Group proteins.

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Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z deposition at Key Regulatory Genes

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Molecular Plant 2018年第6期11卷 815-832页

作者： Angeles Gomez-Zambrano Pedro Crevillen Jose M. Franco-Zorrilla Juan A. Lopez Jordi Moreno-Romero Pawel Roszak Juan Santos-Gonzalez Silvia Jurado Jesus Vazquez Claudia Kohler Roberto Solano Manuel Pineiro Jose A. Jarillo centro de biotecnologia y genomica de plantas Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) Campus Montegancedo UPM Pozuelo de Alarcon 28223 Madrid Spain Plant Molecular Genetics department and Genomics Unit Centro Nacional de Biotecnologia Consejo Superior de Investigaciones Cientfficas 28049 Madrid Spain Proteomics Unit Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) 28029 Madrid Spain department of Plant Biology Uppsala BioCenter Swedish University of Agricultural Sciences and Linnean Center for Plant Biology Uppsala 75652 Sweden Laboratory of Cardiovascular Proteomics Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) 28029 Madrid Spain Instituto de Bioquimica Vegetal y Fotosintesis Consejo Superior de Investigaciones Cientfficas and Universidad de Sevilla 41092 Sevilla Spain Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB Campus UAB Bellaterra Barcelona Spain The Sainsbury Laboratory Cambridge CB2 1LR UK

deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.

关键词： Arabidopsis SWC4 chromatin SWR1 complex H2A.Z deposition flowering time

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