Why and How to Dig into Plant Metabolite–Protein Interactions
Tài liệu tham khảo
Sumner, 2015, Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects, Nat. Prod. Rep., 32, 212, 10.1039/C4NP00072B
Fernie, 2017, The genetics of plant metabolism, Annu. Rev. Genet., 51, 287, 10.1146/annurev-genet-120116-024640
Lacchini, 2020, Combinatorial control of plant specialized metabolism: mechanisms, functions, and consequences, Annu. Rev. Cell Dev. Biol., 36, 291, 10.1146/annurev-cellbio-011620-031429
Schläpfer, 2017, Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants, Plant Physiol., 173, 2041, 10.1104/pp.16.01942
Erb, 2020, Plant secondary metabolites as defenses, regulators, and primary metabolites - the blurred functional trichotomy, Plant Physiol., 184, 39, 10.1104/pp.20.00433
Nakabayashi, 2015, Integrated metabolomics for abiotic stress responses in plants, Curr. Opin. Plant Biol., 24, 10, 10.1016/j.pbi.2015.01.003
Tenenboim, 2016, Omic relief for the biotically stressed: metabolomics of plant biotic interactions, Trends Plant Sci., 21, 781, 10.1016/j.tplants.2016.04.009
Kosmacz, 2020, Towards a functional understanding of the plant metabolome, Curr. Opin. Plant Biol., 55, 47, 10.1016/j.pbi.2020.02.005
Jia, 2019, Anchorene is a carotenoid-derived regulatory metabolite required for anchor root formation in Arabidopsis, Sci. Adv., 5, 10.1126/sciadv.aaw6787
Dickinson, 2019, β-Cyclocitral is a conserved root growth regulator, Proc. Natl. Acad. Sci. U. S. A., 116, 10563, 10.1073/pnas.1821445116
Wang, 2019, The apocarotenoid metabolite zaxinone regulates growth and strigolactone biosynthesis in rice, Nat. Commun., 10, 810, 10.1038/s41467-019-08461-1
Li, 2018, The decoration of specialized metabolites influences stylar development, eLife, 7, 10.7554/eLife.38611
Katz, 2020, Diverse allyl glucosinolate catabolites independently influence root growth and development, Plant Physiol., 183, 1376, 10.1104/pp.20.00170
Katz, 2015, The glucosinolate breakdown product indole-3-carbinol acts as an auxin antagonist in roots of Arabidopsis thaliana, Plant J., 82, 547, 10.1111/tpj.12824
Francisco, 2016, The defense metabolite, allyl glucosinolate, modulates Arabidopsis thaliana biomass dependent upon the endogenous glucosinolate pathway, Front. Plant Sci., 7, 774, 10.3389/fpls.2016.00774
Malinovsky, 2017, An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway, eLife, 6, 10.7554/eLife.29353
Jensen, 2015, Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis, Front. Plant Sci., 6, 697, 10.3389/fpls.2015.00697
Salehin, 2019, Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels, Nat. Commun., 10, 4021, 10.1038/s41467-019-12002-1
Kim, 2020, Glucosinolate and phenylpropanoid biosynthesis are linked by proteasome-dependent degradation of PAL, New Phytol., 225, 154, 10.1111/nph.16108
Kim, 2015, Indole glucosinolate biosynthesis limits phenylpropanoid accumulation in Arabidopsis thaliana, Plant Cell, 27, 1529, 10.1105/tpc.15.00127
Soubeyrand, 2018, The peroxidative cleavage of kaempferol contributes to the biosynthesis of the benzenoid moiety of ubiquinone in plants, Plant Cell, 30, 2910, 10.1105/tpc.18.00688
Steenackers, 2017, cis-Cinnamic acid is a novel, natural auxin efflux inhibitor that promotes lateral root formation, Plant Physiol., 173, 552, 10.1104/pp.16.00943
Hu, 2018, Plant iron acquisition strategy exploited by an insect herbivore, Science, 361, 694, 10.1126/science.aat4082
Jain, 2016, ATPase-modulated stress granules contain a diverse proteome and substructure, Cell, 164, 487, 10.1016/j.cell.2015.12.038
Choi, 2014, Identification of a plant receptor for extracellular ATP, Science, 343, 290, 10.1126/science.343.6168.290
Chen, 2017, Extracellular ATP elicits DORN1-mediated RBOHD phosphorylation to regulate stomatal aperture, Nat. Commun., 8, 2265, 10.1038/s41467-017-02340-3
Tripathi, 2018, Extracellular ATP acts on jasmonate signaling to reinforce plant defense, Plant Physiol., 176, 511, 10.1104/pp.17.01477
Jewell, 2019, Extracellular ATP shapes a defense-related transcriptome both independently and along with other defense signaling pathways, Plant Physiol., 179, 1144, 10.1104/pp.18.01301
Toyota, 2018, Glutamate triggers long-distance, calcium-based plant defense signaling, Science, 361, 1112, 10.1126/science.aat7744
Futuyma, 2009, Macroevolution and the biological diversity of plants and herbivores, Proc. Natl. Acad. Sci. U. S. A., 106, 18054, 10.1073/pnas.0904106106
Jander, 2018, Revisiting plant-herbivore co-evolution in the molecular biology era, Vol. 47, 361
Leong, 2017, Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism, Curr. Opin. Struct. Biol., 47, 105, 10.1016/j.sbi.2017.07.005
Zhang, 2008, The molecular cloning of artemisinic aldehyde Delta11(13) reductase and its role in glandular trichome-dependent biosynthesis of artemisinin in Artemisia annua, J. Biol. Chem., 283, 21501, 10.1074/jbc.M803090200
Sirikantaramas, 2008, Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants, Proc. Natl. Acad. Sci. U. S. A., 105, 6782, 10.1073/pnas.0801038105
Panter, 2018, Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria, Chem. Sci., 9, 4898, 10.1039/C8SC01325J
Tian, 2019, A gossypol biosynthetic intermediate disturbs plant defence response, Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 374, 10.1098/rstb.2018.0319
Itkin, 2011, GLYCOALKALOID METABOLISM1 is required for steroidal alkaloid glycosylation and prevention of phytotoxicity in tomato, Plant Cell, 23, 4507, 10.1105/tpc.111.088732
Stringlis, 2018, MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health, Proc. Natl. Acad. Sci. U. S. A., 115, E5213, 10.1073/pnas.1722335115
Hu, 2018, Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota, Nat. Commun., 9, 2738, 10.1038/s41467-018-05122-7
Stringlis, 2019, The age of coumarins in plant-microbe interactions, Plant Cell Physiol., 60, 1405, 10.1093/pcp/pcz076
Huang, 2019, A specialized metabolic network selectively modulates Arabidopsis root microbiota, Science, 364, 10.1126/science.aau6389
Yu, 2019, Rhizosphere-associated pseudomonas suppress local root immune responses by gluconic acid-mediated lowering of environmental pH, Curr. Biol., 29, 3913, 10.1016/j.cub.2019.09.015
Sugimoto, 2019, A metagenomic strategy for harnessing the chemical repertoire of the human microbiome, Science, 366, 10.1126/science.aax9176
Lupini, 2018, Coumarin enhances nitrate uptake in maize roots through modulation of plasma membrane H+-ATPase activity, Plant Biol., 20, 390, 10.1111/plb.12674
Pollier, 2019, The MYB transcription factor Emission of Methyl Anthranilate 1 stimulates emission of methyl anthranilate from Medicago truncatula hairy roots, Plant J., 99, 637, 10.1111/tpj.14347
Li, 2020, Methyl anthranilate: a novel quorum sensing inhibitor and anti-biofilm agent against Aeromonas sobria, Food Microbiol., 86, 10.1016/j.fm.2019.103356
Kong, 2012, Regulatory switch enforced by basic helix-loop-helix and ACT-domain mediated dimerizations of the maize transcription factor R, Proc. Natl. Acad. Sci. U. S. A., 109, E2091, 10.1073/pnas.1205513109
Kim, 2020, Transcription factor-based biosensors and inducible systems in non-model bacteria: current progress and future directions, Curr. Opin. Biotechnol., 64, 39, 10.1016/j.copbio.2019.09.009
Libis, 2016, Sensing new chemicals with bacterial transcription factors, Curr. Opin. Microbiol., 33, 105, 10.1016/j.mib.2016.07.006
Koch, 2019, Custom-made transcriptional biosensors for metabolic engineering, Curr. Opin. Biotechnol., 59, 78, 10.1016/j.copbio.2019.02.016
Hanko, 2020, A genome-wide approach for identification and characterisation of metabolite-inducible systems, Nat. Commun., 11, 1213, 10.1038/s41467-020-14941-6
Li, 2010, Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses, Cell, 143, 639, 10.1016/j.cell.2010.09.048
Piazza, 2018, A map of protein-metabolite interactions reveals principles of chemical communication, Cell, 172, 358, 10.1016/j.cell.2017.12.006
Diether, 2019, Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli, Mol. Syst. Biol., 15, 10.15252/msb.20199008
Li, 2020, Systematic mapping of protein-metabolite interactions with mass spectrometry-based techniques, Curr. Opin. Biotechnol., 64, 24, 10.1016/j.copbio.2019.09.002
Luzarowski, 2019, Emerging strategies for the identification of protein–metabolite interactions, J. Exp. Bot., 70, 4605, 10.1093/jxb/erz228
Diether, 2017, Towards detecting regulatory protein–metabolite interactions, Curr. Opin. Microbiol., 39, 16, 10.1016/j.mib.2017.07.006
Luzarowski, 2017, Affinity purification with metabolomic and proteomic analysis unravels diverse roles of nucleoside diphosphate kinases, J. Exp. Bot., 68, 3487, 10.1093/jxb/erx183
Sterlin, 2019, Optimized small-molecule pull-downs define MLBP1 as an acyl-lipid-binding protein, Plant J., 98, 928, 10.1111/tpj.14272
Pellecchia, 2008, Perspectives on NMR in drug discovery: a technique comes of age, Nat. Rev. Drug Discov., 7, 738, 10.1038/nrd2606
Nikolaev, 2016, Systematic identification of protein–metabolite interactions in complex metabolite mixtures by ligand-detected nuclear magnetic resonance spectroscopy, Biochemistry, 55, 2590, 10.1021/acs.biochem.5b01291
Ong, 2002, Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol. Cell. Proteomics, 1, 376, 10.1074/mcp.M200025-MCP200
Ong, 2009, Identifying the proteins to which small-molecule probes and drugs bind in cells, Proc. Natl. Acad. Sci. U. S. A., 106, 4617, 10.1073/pnas.0900191106
Manohar, 2014, Identification of multiple salicylic acid-binding proteins using two high throughput screens, Front. Plant Sci., 5, 777
Choi, 2019, A genome-wide screen for human salicylic acid (SA)-binding proteins reveals targets through which SA may influence development of various diseases, Sci. Rep., 9
Park, 2013, Cyclophilin 20-3 relays a 12-oxo-phytodienoic acid signal during stress responsive regulation of cellular redox homeostasis, Proc. Natl. Acad. Sci. U. S. A., 110, 9559, 10.1073/pnas.1218872110
Chidley, 2011, A yeast-based screen reveals that sulfasalazine inhibits tetrahydrobiopterin biosynthesis, Nat. Chem. Biol., 7, 375, 10.1038/nchembio.557
Cottier, 2011, The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: potential and limitations, Front. Plant Sci., 2, 101
Lomenick, 2009, Target identification using drug affinity responsive target stability (DARTS), Proc. Natl. Acad. Sci. U. S. A., 106, 21984, 10.1073/pnas.0910040106
Martinez Molina, 2013, Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay, Science, 341, 84, 10.1126/science.1233606
Savitski, 2014, Tracking cancer drugs in living cells by thermal profiling of the proteome, Science, 346, 10.1126/science.1255784
Dziekan, 2019, Identifying purine nucleoside phosphorylase as the target of quinine using cellular thermal shift assay, Sci. Transl. Med., 11, 10.1126/scitranslmed.aau3174
Strickland, 2013, Thermodynamic analysis of protein-ligand binding interactions in complex biological mixtures using the stability of proteins from rates of oxidation, Nat. Protoc., 8, 148, 10.1038/nprot.2012.146
West, 2008, Thermodynamic analysis of protein stability and ligand binding using a chemical modification- and mass spectrometry-based strategy, Anal. Chem., 80, 4175, 10.1021/ac702610a
Huber, 2015, Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling, Nat. Methods, 12, 1055, 10.1038/nmeth.3590
Zhang, 2016, Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis, Proc. Natl. Acad. Sci. U. S. A., 113, E41, 10.1073/pnas.1521248112
Piazza, 2019, LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes, bioRxiv
Veyel, 2018, PROMIS, global analysis of protein-metabolite interactions using size separation in Arabidopsis thaliana, J. Biol. Chem., 293, 12440, 10.1074/jbc.RA118.003351
Kosmacz, 2018, Interaction of 2′,3′-cAMP with Rbp47b plays a role in stress granule formation, Plant Physiol., 177, 411
Sridharan, 2019, Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP, Nat. Commun., 10, 1155, 10.1038/s41467-019-09107-y
Niu, 2018, Protein extraction methods shape much of the extracted proteomes, Front. Plant Sci., 9, 802, 10.3389/fpls.2018.00802
Hu, 2015, Advances in plant proteomics toward improvement of crop productivity and stress resistance, Front. Plant Sci., 6, 209, 10.3389/fpls.2015.00209
Zhang, 2019, Arabidopsis proteome and the mass spectral assay library. Sci, Data, 6, 278
Mergner, 2020, Mass-spectrometry-based draft of the Arabidopsis proteome, Nature, 579, 409, 10.1038/s41586-020-2094-2
O'Donnell, 2020, A neurotransmitter produced by gut bacteria modulates host sensory behaviour, Nature, 583, 415, 10.1038/s41586-020-2395-5
Schretter, 2018, A gut microbial factor modulates locomotor behaviour in Drosophila, Nature, 563, 402, 10.1038/s41586-018-0634-9