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

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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Role of 9-Lipoxygenase and α-Dioxygenase Oxylipin Pathways as Modulators of Local and Systemic defense

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Molecular Plant 2012年第4期5卷 914-928页

作者： Jorge Vicente Tomas Cascon Begonya Vicedo Pilar Garcia-Agustin Mats Hamberg Carmen Castresana department of Plant Molecular Genetics Centro National de Biotecnologia (CNB-CSIC) Darwin 3 28049 Madrid Spain Grupo de Bioquimica y biotecnologia vegetal Area de Fisiologfa Vegetal Departarnento de Ciencias Agrarias y del Medio Natural. ESTCE Universitat Jaume I Campus de Riu Sec. 12071 Castellon Spain Division of Physiological Chemistry II Department of Medical Biochemistry and Biophysics Karolinska Institutet S-171 77 Stockholm Sweden

Plant 9-1ipoxygenases （9-LOX） and α-dioxygenases （α-DOX） initiate the synthesis of oxylipins after bacterial infection. Here, the role of these enzymes in plants＇ defense was investigated using individual Arabidopsis thaliana Ioxl and doxl mutants and a double Ioxl doxl mutant. Studies with Pseudomonas syringae pv. tomato （Pst） revealed the enhanced susceptibility of Ioxl to the virulent strain Pst DC3000 and the partial impairment of Ioxl and doxl mutants to activate systemic acquired resistance. Notably, both defects were enhanced in the Ioxl doxl plants as compared with individual mutants. We found that pre-treatment with 9-LOX- and α-DOX-generated oxylipins protected plant tissues against bacterial infection. The strongest effect in this respect was exerted by 9-ketooctadecatrienoic acid （9-KOT）, which is produced from linolenic acid by 9-LOX. Quantification of 9-KOT revealed its accumulation after bacterial infection. The levels were reduced in Ioxl and Ioxl doxl plants but strongly increased in the doxl mutant due to metabolic interaction of the two pathways. Transcriptional analyses indicated that 9-KOT pre-treatment modifies hormone homeostasis during bacterial infection. The nature of the changes detected suggested that 9-KOT interferes with the hormonal changes caused by bacterial effectors. This notion was substantiated by the finding that 9-KOT failed to reduce the growth of PstDC3OOOhrpA, a mutant compromised in effector secretion, and of the avirulent strain Pst DC3000 avrRpml. Further support for the action of the 9-LOX- and α-DOX-oxylipin pathways as modulators of hormone homeostasis was the ob- servation that Ioxl doxl seedlings are hypersensitive to the growth-inhibitory effect of ABA and showed enhanced ac- tivation of ABA-inducible marker genes as compared with wild-type plants.

关键词： oxylipins plant defense ABA Arabidopsis.

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DNA features beyond the transcription factor binding site specify target recognition by plant MYC2-related bHLH proteins

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Plant Communications 2021年第6期2卷 27-43页

作者： Irene Lopez-Vidriero Marta Godoy Joaquin Grau Maria Penuelas Roberto Solano Jose M.Franco-Zorrilla Genomics Unit Centro Nacional de BiotecnologiaCSICC/Darwin 328049 MadridSpain department of Plant Molecular Genetics Centro Nacional de BiotecnologiaCSICC/Darwin 328049 MadridSpain

Transcription factors(TFs)regulate gene expression by binding to cis-regulatory sequences in the promoters of target *** research is helping to decipher in part the cis-regulatory code in eukaryotes,including plants,but it is not yet fully understood how paralogous TFs select their *** we addressed this question by studying several proteins of the basic helix-loop-helix(bHLH)family of plant TFs,all of which recognize the same DNA *** focused on the MYC-related group of bHLHs,that redundantly regulate the jasmonate(JA)signaling pathway,and we observed a high correspondence between DNA-binding profiles in vitro and MYC function in *** demonstrated that A/T-rich modules flanking the MYC-binding motif,conserved from bryophytes to higher plants,are essential for TF recogni*** observed particular DNA-shape features associated with A/T modules,indicating that the DNA shape may contribute to MYC DNA *** extended this analysis to 20 additional bHLHs and observed correspondence between in vitro binding and protein function,but it could not be attributed to A/T modules as in *** conclude that different bHLHs may have their own codes for DNA binding and specific selection of targets that,at least in the case of MYCs,depend on the TF-DNA interplay.

关键词： transcription factor bHLH target specificity plants

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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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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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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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Building the DREAM interactome

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Science China(Life Sciences) 2011年第8期54卷 786-792页

作者： Marcos RIVAS Diego VILLAR Paz GONZLEZ Xosé M.DOPAZO Britt MELLSTROM José R.NARANJO department of Molecular and Cellular Biology National Center of BiotechnologyConsejo Superior Investigaciones Cientificas centro Investigacion Biomedica En Red de Enfermedades Neurodegenerativas-centro Nacional de biotecnologia

DREAM/calsenilin/KChIP3 is a calcium binding protein of the neuronal calcium sensor *** interacts with DRE(downstream regulatory element) sites in the DNA to regulate transcription and with many proteins to exert specialized functions in different subcellular *** from different laboratories has identified a growing list of interacting proteins that constitutes the DREAM *** knowledge of these interactions has greatly contributed to the understanding of the various physiological functions of DREAM.

关键词： calsenilin KChIP3 protein-protein interaction

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Repression of the Auxin Response Pathway Increases Arabidopsis Susceptibility to Necrotrophic Fungi

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Molecular Plant 2008年第3期1卷 496-509页

作者： Francisco Llorente Paul M usksktt Andrea Sanchez-Vallet Gemma Lopez Brisa Ramos Clara Sanchez-Rodriguez Lucia Jorda Jane Parker Antonio Molina centro de biotecnologia y Genbmica de Plantas (CBGP) Departamento de Biotecnologia-UPM ETS Ingenieros Agrbnomos Avda Complutense E-28040Madrid Spain department of Plant-Microbe Interactions Max Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany

In plants, resistance to necrotrophic pathogens depends on the interplay between different hormone systems, such as those regulated by salicylic acid （SA）, jasmonic acid （JA）, ethylene, and abscisic acid. Repression of auxin signaling by the SA pathway was recently shown to contribute to antibacterial resistance. Here, we demonstrate that Arabidopsis auxin signaling mutants axrl, axr2, and axr6 that have defects in the auxin-stimulated SCF （Skpl-Cullin- F-box） ubiquitination pathway exhibit increased susceptibility to the necrotrophic fungi Plectosphaerella cucumerina and Botrytis cinerea. Also, stabilization of the auxin transcriptional repressor AXR3 that is normally targeted for removal by the SCF-ubiquitin/proteasome machinery occurs upon P. cucumerina infection. Pharmacological inhibition of auxin transport or proteasome function each compromise necrotroph resistance of wild-type plants to a similar extent as in non-treated auxin response mutants. These results suggest that auxin signaling is important for resistance to the necrotro- phic fungi P. cucumerina and B. cinerea. SGTlb （one of two Arabidopsis SGT1 genes encoding HSP90/HSC70 co-chaperones） promotes the functions of SCF E3-ubiquitin ligase complexes in auxin and JA responses and resistance conditioned by certain Resistance （R） genes to biotrophic pathogens. We find that sgtlb mutants are as resistant to P. cucumerina as wild-type plants. Conversely, auxin/SCF signaling mutants are uncompromised in RPP4-triggered resistance to the obligate biotrophic oomycete, Hyaloperonospora parasitica. Thus, the predominant action of SGTlb in R gene-conditioned resis- tance to oomycetes appears to be at a site other than assisting SCF E3-ubiquitin ligases. However, genetic additivity of sgtlb axrl double mutants in susceptibility to H. parasitica suggests that SCF-mediated ubiquitination contributes to lim- iting biotrophic pathogen colonization once plant-pathogen compatibility is established.

关键词： plant defense innate immunity necrotrophic fungi auxin signaling proteasome.

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A Single JAZ Repressor Controls the Jasmonate Pathway in Marchantia polymorpha

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Molecular Plant 2019年第2期12卷 185-198页

作者： Isabel Monte Jose M. Franco-Zorrilla Gloria Garcia-Casado Angel M. Zamarreno Jose M. Garcia-Mina Ryuichi Nishihama Takayuki Kohchi Roberto Solano department of Plant Molecular Genetics Centro Nacional de Biotecnologia Consejo Superior de Investigaciones Cientificas (CNB-CSIC) 28049 Madrid Spain Genomics Unit Centro Nacional de Biotecnologia Consejo Superior de Investigaciones Cientificas (CNB-CSIC) 28049 Madrid Spain Environmental Biology department University of Navarra Navarre Spain Graduate School of Biostudies Kyoto University Kyoto 606-8502 Japan

JAZ proteins are negative regulators of jasm onate responses,acting both as repressors of transcription factors and as co-receptors of JA-lle. The high redundancy of JAZ genes in angiosperms has hindered the characterization of a complete depletion of JAZ function. Moreover, the recent discovery that dn- OPDA is the jasmonate ligand in Marchantia polymorpha demonstrates that JA-lle is not the sole COI1/ JAZ ligand in land plants and highlights the importance of studying JAZ co-receptors in bryophytes? Here, we have exploited the low gene redundancy of the liverwort M. polymorpha to characterize the single MpJ4Z in this early diverging plant lineage. We clarify the phylogenetic history of the TIFY family, demonstrate that MpJAZ is the ortholog of AtJAZ with a conserved function, and characterize its repressor activity of dn-OPDA resp on ses. Our results show that, con sistent with previous findings in Arabidopsis, MpJAZ represses jasmonates biosynthesis, senescence, and plant defenses, and promotes cell growth and reproductive fitness, highlighting the power of studies in Marchantia.

关键词： Jasmonate repressors Marchantia Hormone signaling evolution gene redundancy

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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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