Extensive signal integration by the phytohormone protein network.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
06
06
2019
accepted:
14
04
2020
pubmed:
3
7
2020
medline:
18
7
2020
entrez:
3
7
2020
Statut:
ppublish
Résumé
Plant hormones coordinate responses to environmental cues with developmental programs
Identifiants
pubmed: 32612234
doi: 10.1038/s41586-020-2460-0
pii: 10.1038/s41586-020-2460-0
doi:
Substances chimiques
Arabidopsis Proteins
0
Plant Growth Regulators
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
271-276Subventions
Organisme : European Research Council
Pays : International
Commentaires et corrections
Type : ErratumIn
Références
Krouk, G. et al. A framework integrating plant growth with hormones and nutrients. Trends Plant Sci. 16, 178–182 (2011).
pubmed: 21393048
doi: 10.1016/j.tplants.2011.02.004
Peleg, Z. & Blumwald, E. Hormone balance and abiotic stress tolerance in crop plants. Curr. Opin. Plant Biol. 14, 290–295 (2011).
pubmed: 21377404
doi: 10.1016/j.pbi.2011.02.001
Lumba, S. et al. A mesoscale abscisic acid hormone interactome reveals a dynamic signaling landscape in Arabidopsis. Dev. Cell 29, 360–372 (2014).
pubmed: 24823379
doi: 10.1016/j.devcel.2014.04.004
Nemhauser, J. L., Hong, F. & Chory, J. Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell 126, 467–475 (2006).
doi: 10.1016/j.cell.2006.05.050
pubmed: 16901781
Orchard, S. et al. The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 42, D358–D363 (2014).
pubmed: 24234451
doi: 10.1093/nar/gkt1115
Yu, H. et al. High-quality binary protein interaction map of the yeast interactome network. Science 322, 104–110 (2008).
pubmed: 18719252
pmcid: 2746753
doi: 10.1126/science.1158684
Altmann, M., Altmann, S., Falter, C. & Falter-Braun, P. High-quality yeast-2-hybrid interaction network mapping. Curr. Protoc. Plant Biol. 3, e20067 (2018).
pubmed: 29944780
doi: 10.1002/cppb.20067
Weßling, R. et al. Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe 16, 364–375 (2014).
pubmed: 25211078
pmcid: 4191710
doi: 10.1016/j.chom.2014.08.004
Pruneda-Paz, J. L. et al. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep. 8, 622–632 (2014).
pubmed: 25043187
pmcid: 4125603
doi: 10.1016/j.celrep.2014.06.033
Arabidopsis Interactome Mapping Consortium. Evidence for network evolution in an Arabidopsis interactome map. Science 333, 601–607 (2011).
pmcid: 3170756
doi: 10.1126/science.1203877
Braun, P. et al. An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91–97 (2009).
doi: 10.1038/nmeth.1281
pubmed: 19060903
Braun, P. Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays. Proteomics 12, 1499–1518 (2012).
pubmed: 22589225
doi: 10.1002/pmic.201100598
Oughtred, R. et al. The BioGRID interaction database: 2019 update. Nucleic Acids Res. 47 (D1), D529–D541 (2019).
pubmed: 30476227
doi: 10.1093/nar/gky1079
Barabási, A.-L., Gulbahce, N. & Loscalzo, J. Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 12, 56–68 (2011).
pubmed: 21164525
pmcid: 3140052
doi: 10.1038/nrg2918
Girvan, M. & Newman, M. E. Community structure in social and biological networks. Proc. Natl Acad. Sci. USA 99, 7821–7826 (2002).
pubmed: 12060727
pmcid: 122977
doi: 10.1073/pnas.122653799
Cutler, S. R., Rodriguez, P. L., Finkelstein, R. R. & Abrams, S. R. Abscisic acid: emergence of a core signaling network. Annu. Rev. Plant Biol. 61, 651–679 (2010).
pubmed: 20192755
doi: 10.1146/annurev-arplant-042809-112122
Deikman, J. & Hammer, P. E. Induction of anthocyanin accumulation by cytokinins in Arabidopsis thaliana. Plant Physiol. 108, 47–57 (1995).
pubmed: 12228453
pmcid: 157304
doi: 10.1104/pp.108.1.47
Guzmán, P. & Ecker, J. R. Exploiting the triple response of Arabidopsis to identify ethylene-related mutants. Plant Cell 2, 513–523 (1990).
pubmed: 2152173
pmcid: 159907
Vlot, A. C., Dempsey, D. A. & Klessig, D. F. Salicylic acid, a multifaceted hormone to combat disease. Annu. Rev. Phytopathol. 47, 177–206 (2009).
pubmed: 19400653
doi: 10.1146/annurev.phyto.050908.135202
Lumba, S., Cutler, S. & McCourt, P. Plant nuclear hormone receptors: a role for small molecules in protein–protein interactions. Annu. Rev. Plant Biol. 26, 445–469 (2010).
Tischer, S. V. et al. Combinatorial interaction network of abscisic acid receptors and coreceptors from Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 114, 10280–10285 (2017).
pubmed: 28874521
pmcid: 5617281
doi: 10.1073/pnas.1706593114
Aleman, F. et al. An ABA-increased interaction of the PYL6 ABA receptor with MYC2 transcription factor: a putative link of ABA and JA signaling. Sci. Rep. 6, 28941 (2016).
pubmed: 27357749
pmcid: 4928087
doi: 10.1038/srep28941
Zhao, Y. et al. The ABA receptor PYL8 promotes lateral root growth by enhancing MYB77-dependent transcription of auxin-responsive genes. Sci. Signal. 7, ra53 (2014).
pubmed: 24894996
pmcid: 4298826
doi: 10.1126/scisignal.2005051
Née, G. et al. DELAY OF GERMINATION1 requires PP2C phosphatases of the ABA signalling pathway to control seed dormancy. Nat. Commun. 8, 72 (2017).
pubmed: 28706187
pmcid: 5509711
doi: 10.1038/s41467-017-00113-6
Kuai, X., MacLeod, B. J. & Després, C. Integrating data on the Arabidopsis NPR1/NPR3/NPR4 salicylic acid receptors; a differentiating argument. Front. Plant Sci. 6, 235 (2015).
pubmed: 25914712
pmcid: 4392584
doi: 10.3389/fpls.2015.00235
Ding, Y. et al. Opposite roles of salicylic acid receptors NPR1 and NPR3/NPR4 in transcriptional regulation of plant immunity. Cell 173, 1454–1467 (2018).
pubmed: 29656896
doi: 10.1016/j.cell.2018.03.044
Hermann, M. et al. The Arabidopsis NIMIN proteins affect NPR1 differentially. Front Plant Sci 4, 88 (2013).
pubmed: 23630533
pmcid: 3624081
doi: 10.3389/fpls.2013.00088
Waters, M. T., Gutjahr, C., Bennett, T. & Nelson, D. C. Strigolactone signaling and evolution. Annu. Rev. Plant Biol. 68, 291–322 (2017).
pubmed: 28125281
doi: 10.1146/annurev-arplant-042916-040925
Scaffidi, A. et al. Strigolactone hormones and their stereoisomers signal through two related receptor proteins to induce different physiological responses in Arabidopsis. Plant Physiol. 165, 1221–1232 (2014).
pubmed: 24808100
pmcid: 4081333
doi: 10.1104/pp.114.240036
Villaécija-Aguilar, J. A. et al. SMAX1/SMXL2 regulate root and root hair development downstream of KAI2-mediated signalling in Arabidopsis. PLoS Genet. 15, e1008327 (2019).
pubmed: 31465451
pmcid: 6738646
doi: 10.1371/journal.pgen.1008327
Jiang, Z. et al. AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies. Nucleic Acids Res. 39, D1123–D1129 (2011).
pubmed: 21045062
doi: 10.1093/nar/gkq1066
Stark, C. et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 34, D535–D539 (2006).
pubmed: 16381927
doi: 10.1093/nar/gkj109
Venkatesan, K. et al. An empirical framework for binary interactome mapping. Nat. Methods 6, 83–90 (2009).
pubmed: 19060904
doi: 10.1038/nmeth.1280
Barabási, A. L. & Oltvai, Z. N. Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113 (2004).
pubmed: 14735121
doi: 10.1038/nrg1272
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
pubmed: 14597658
pmcid: 403769
doi: 10.1101/gr.1239303
Cheng, C. Y. et al. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J. 89, 789–804 (2017).
pubmed: 27862469
doi: 10.1111/tpj.13415
Csárdi, G. & Nepusz, T. The igraph software package for complex network research. InterJ. Complex Syst. 1695, 1–9 (2006).
Falcon, S. & Gentleman, R. Using GOstats to test gene lists for GO term association. Bioinformatics 23, 257–258 (2007).
doi: 10.1093/bioinformatics/btl567
pubmed: 17098774
Chatr-aryamontri, A. et al. The BioGRID interaction database: 2017 update. Nucleic Acids Res. 45 (D1), D369–D379 (2017).
pubmed: 27980099
doi: 10.1093/nar/gkw1102
Edwards, K., Johnstone, C. & Thompson, C. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res. 19, 1349 (1991).
pubmed: 2030957
pmcid: 333874
doi: 10.1093/nar/19.6.1349
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
doi: 10.1038/nmeth.2019
Longair, M. H., Baker, D. A. & Armstrong, J. D. Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes. Bioinformatics 27, 2453–2454 (2011).
pubmed: 21727141
doi: 10.1093/bioinformatics/btr390
Nakata, M. & Ohme-Takagi, M. Quantification of anthocyanin content. Bio Protoc. 4, e1098 (2014).
Wenig, M. et al. Systemic acquired resistance networks amplify airborne defense cues. Nat. Commun. 10, 3813 (2019).
pubmed: 31444353
pmcid: 6707303
doi: 10.1038/s41467-019-11798-2
Belda-Palazón, B. et al. Aminopropyltransferases involved in polyamine biosynthesis localize preferentially in the nucleus of plant cells. PLoS ONE 7, e46907 (2012).
pubmed: 23056524
pmcid: 3466176
doi: 10.1371/journal.pone.0046907
Gehl, C. et al. Quantitative analysis of dynamic protein-protein interactions in planta by a floated-leaf luciferase complementation imaging (FLuCI) assay using binary Gateway vectors. Plant J. 67, 542–553 (2011).
pubmed: 21481030
doi: 10.1111/j.1365-313X.2011.04607.x
Klepikova, A. V., Kasianov, A. S., Gerasimov, E. S., Logacheva, M. D. & Penin, A. A. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J. 88, 1058–1070 (2016).
pubmed: 27549386
doi: 10.1111/tpj.13312
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016); erratum 34, 888 (2016).
doi: 10.1038/nbt.3519
pubmed: 27043002