Profiling of secondary metabolites in root exudates of Arabidopsis thaliana

Phytochemistry

Volumn 108, Issue , 2014, Pages 35-46

  Strehmel, Nadine ^a   Böttcher, Christoph ^a,b   Schmidt, Stephan ^a   Scheel, Dierk ^a  

^a LEIBNIZ INSTITUTE OF PLANT BIOCHEMISTRY   (Germany)

^b INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

Author keywords

Arabidopsis thaliana; Brassicaceae; LC MS; Metabolite profiling; Root exudates; Secondary metabolism; Structure elucidation

Indexed keywords

ARABIDOPSIS THALIANA; BRASSICACEAE;

AROMATIC AMINO ACID; CYCLOPENTANE DERIVATIVE; DIPEPTIDE; GLUCOSINOLATE; INDOLE DERIVATIVE; JASMONIC ACID; NUCLEOSIDE; OXYLIPIN; SALICYLIC ACID;

ARABIDOPSIS; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PLANT ROOT; SOLID PHASE EXTRACTION; TANDEM MASS SPECTROMETRY;

AMINO ACIDS, AROMATIC; ARABIDOPSIS; CYCLOPENTANES; DIPEPTIDES; GLUCOSINOLATES; INDOLES; MOLECULAR STRUCTURE; NUCLEOSIDES; OXYLIPINS; PLANT ROOTS; SALICYLIC ACID; SOLID PHASE EXTRACTION; TANDEM MASS SPECTROMETRY;

EID: 84911476750     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2014.10.003     Document Type: Article

References (64)

1. R.N. Arteca, and J.M. Arteca A novel method for growing Arabidopsis thaliana plants hydroponically Physiol. Plant. 108 2000 188 193
2. B. Auger, J.-B. Pouvreau, K. Pouponneau, K. Yoneyama, G. Montiel, B. Le Bizec, K. Yoneyama, P. Delavault, R. Delourme, and P. Simier Germination stimulants of Phelipanche ramosa in the rhizosphere of Brassica napus are derived from the glucosinolate pathway Mol. Plant Microbe Interact. 25 2012 993 1004
3. M.S. Aulakh, R. Wassmann, C. Bueno, J. Kreuzwieser, and H. Rennenberg Characterization of root exudates at different growth stages of fen rice (Oryza sativa L.) cultivars Plant Biol. 3 2001 139 148
4. D.V. Badri, J.M. Chaparro, D.K. Manter, E. Martinoia, and J.M. Vivanco Influence of ATP-binding cassette transporters in root exudation of phytoalexins, signals, and in disease resistance Front. Plant Sci. 3 2012 149
5. D.V. Badri, J.M. Chaparro, R. Zhang, Q. Shen, and J.M. Vivanco Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome J. Biol. Chem. 288 2013 4502 4512
6. D.V. Badri, and J.M. Vivanco Regulation and function of root exudates Plant Cell Environ. 32 2009 666 681
7. U. Baetz, and E. Martinoia Root exudates: the hidden part of plant defense Trends Plant Sci. 19 2014 90 98
8. H.P. Bais, T.L. Weir, L.G. Perry, S. Gilroy, and J.M. Vivanco The role of root exudates in rhizosphere interactions with plants and other organisms Annu. Rev. Plant Biol. 57 2006 233 266
9. M. Bartsch, P. Bednarek, P.D. Vivancos, B. Schneider, E. von Roepenack-Lahaye, C.H. Foyer, E. Kombrink, D. Scheel, and J.E. Parker Accumulation of isochorismate-derived 2,3-dihydroxybenzoic 3-O-beta-d-xyloside in Arabidopsis resistance to pathogens and ageing of leaves J. Biol. Chem. 285 2010 25654 25665
10. P. Bednarek, M. Pislewska-Bednarek, A. Svatos, B. Schneider, J. Doubsky, M. Mansurova, M. Humphry, C. Consonni, R. Panstruga, A. Sanchez-Vallet, A. Molina, and P. Schulze-Lefert A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense Science 323 2009 101 106
11. P. Bednarek, B. Schneider, A. Svatos, N.J. Oldham, and K. Hahlbrock Structural complexity, differential response to infection, and tissue specificity of indolic and phenylpropanoid secondary metabolism in Arabidopsis roots Plant Physiol. 138 2005 1058 1070
12. M.L. Biedrzycki, T.A. Jilany, S.A. Dudley, and H.P. Bais Root exudates mediate kin recognition in plants Commun. Integr. Biol. 3 2010 28 35
13. C. Bottcher, A. Chapman, F. Fellermeier, M. Choudhary, D. Scheel, and E. Glawischnig The biosynthetic pathway of indole-3-carbaldehyde and indole-3-carboxylic acid derivatives in Arabidopsis Plant Physiol. 165 2014 841 853
14. H.J. Bouwmeester, C. Roux, J.A. Lopez-Raez, and G. Becard Rhizosphere communication of plants, parasitic plants and AM fungi Trends Plant Sci. 12 2007 224 230
15. P.D. Brown, J.G. Tokuhisa, M. Reichelt, and J. Gershenzon Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana Phytochemistry 62 2003 471 481
16. J.M. Chaparro, D.V. Badri, M.G. Bakker, A. Sugiyama, D.K. Manter, and J.M. Vivanco Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions PLoS One 8 2013 e55731
17. S.J. Conn, B. Hocking, M. Dayod, B. Xu, A. Athman, S. Henderson, L. Aukett, V. Conn, M.K. Shearer, S. Fuentes, S.D. Tyerman, and M. Gilliham Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants Plant Methods 9 1 2013 4
18. F.D. Dakora, and D.A. Phillips Root exudates as mediators of mineral acquisition in low-nutrient environments Plant Soil 245 2002 35 47
19. D. Faure, D. Vereecke, and J.H.J. Leveau Molecular communication in the rhizosphere Plant Soil 321 2009 279 303
20. S. Floerl, A. Majcherczyk, M. Possienke, K. Feussner, H. Tappe, C. Gatz, I. Feussner, U. Kues, and A. Polle Verticillium longisporum infection affects the leaf apoplastic proteome, metabolome, and cell wall properties in Arabidopsis thaliana PLoS One 7 2012 e31435
21. P. Fourcroy, P. Siso-Terraza, D. Sudre, M. Saviron, G. Reyt, F. Gaymard, A. Abadia, J. Abadia, A. Alvarez-Fernandez, and J.F. Briat Involvement of the ABCG37 transporter in secretion of scopoletin and derivatives by Arabidopsis roots in response to iron deficiency New Phytol. 201 2014 155 167
22. D.M. Gibeaut, J. Hulett, G.R. Cramer, and J.R. Seemann Maximal biomass of Arabidopsis thaliana using a simple, low-maintenance hydroponic method and favorable environmental conditions Plant Phys. 115 1997 317 319
23. S.K. Gidda, O. Miersch, A. Levitin, J. Schmidt, C. Wasternack, and L. Varin Biochemical and molecular characterization of a hydroxyjasmonate sulfotransferase from Arabidopsis thaliana J. Biol. Chem. 278 2003 17895 17900
24. J. Hagemeier, B. Schneider, N.J. Oldham, and K. Hahlbrock Accumulation of soluble and wall-bound indolic metabolites in Arabidopsis thaliana leaves infected with virulent or avirulent Pseudomonas syringae pathovar tomato strains Proc. Natl. Acad. Sci. U. S. A. 98 2001 753 758
25. M.R. Hemm, S.D. Rider, J. Ogas, D.J. Murry, and C. Chapple Light induces phenylpropanoid metabolism in Arabidopsis roots Plant J. 38 2004 765 778
26. L. Jaitz, B. Mueller, G. Koellensperger, D. Huber, E. Oburger, M. Puschenreiter, and S. Hann LC-MS analysis of low molecular weight organic acids derived from root exudation Anal. Bioanal. Chem. 400 2011 2587 2596
27. D.L. Jones, C. Nguyen, and R.D. Finlay Carbon flow in the rhizosphere: carbon trading at the soil-root interface Plant Soil 321 2009 5 33
28. H.W. Jung, T.J. Tschaplinski, L. Wang, J. Glazebrook, and J.T. Greenberg Priming in systemic plant immunity Science 324 2009 89 91
29. K. Kai, B. Shimizu, M. Mizutani, K. Watanabe, and K. Sakata Accumulation of coumarins in Arabidopsis thaliana Phytochemistry 67 2006 379 386
30. W. Kohlen, T. Charnikhova, Q. Liu, R. Bours, M.A. Domagalska, S. Beguerie, F. Verstappen, O. Leyser, H. Bouwmeester, and C. Ruyter-Spira Strigolactones are transported through the xylem and play a key role in shoot architectural response to phosphate deficiency in nonarbuscular mycorrhizal host Arabidopsis Plant Physiol. 155 2011 974 987
31. N.Y. Komarova, K. Thor, A. Gubler, S. Meier, D. Dietrich, A. Weichert, M. Suter Grotemeyer, M. Tegeder, and D. Rentsch AtPTR1 and AtPTR5 transport dipeptides in planta Plant Physiol. 148 2008 856 869
32. A. Lanoue, V. Burlat, G.J. Henkes, I. Koch, U. Schurr, and U.S. Rose De novo biosynthesis of defense root exudates in response to Fusarium attack in barley New Phytol. 185 2010 577 588
33. V. Lipka, J. Dittgen, P. Bednarek, R. Bhat, M. Wiermer, M. Stein, J. Landtag, W. Brandt, S. Rosahl, D. Scheel, F. Llorente, A. Molina, J. Parker, S. Somerville, and P. Schulze-Lefert Pre- and postinvasion defenses both contribute to nonhost resistance in Arabidopsis Science 310 2005 1180 1183
34. D.Q. Liu, C.E. Hop, M.G. Beconi, A. Mao, and S.H. Chiu Use of on-line hydrogen/deuterium exchange to facilitate metabolite identification Rapid Commun. Mass Spectrom. 15 2001 1832 1839
35. D.Q. Liu, L. Wu, M. Sun, and P.A. MacGregor On-line H/D exchange LC-MS strategy for structural elucidation of pharmaceutical impurities J. Pharm. Biomed. Anal. 44 2007 320 329
36. J. Luo, C. Fuell, A. Parr, L. Hill, P. Bailey, K. Elliott, S.A. Fairhurst, C. Martin, and A.J. Michael A novel polyamine acyltransferase responsible for the accumulation of spermidine conjugates in Arabidopsis seed Plant Cell 21 2009 318 333
37. J.F. Ma, P.R. Ryan, and E. Delhaize Aluminium tolerance in plants and the complexing role of organic acids Trends Plant Sci. 6 2001 273 278
38. F. Matsuda, M.Y. Hirai, E. Sasaki, K. Akiyama, K. Yonekura-Sakakibara, N.J. Provart, T. Sakurai, Y. Shimada, and K. Saito AtMetExpress development: a phytochemical atlas of Arabidopsis development Plant Physiol. 152 2010 566 578
39. Y.A. Millet, C.H. Danna, N.K. Clay, W. Songnuan, M.D. Simon, D. Werck-Reichhart, and F.M. Ausubel Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns Plant Cell 22 2010 973 990
40. K. Morreel, O. Dima, H. Kim, F.C. Lu, C. Niculaes, R. Vanholme, R. Dauwe, G. Goeminne, D. Inze, E. Messens, J. Ralph, and W. Boerjan Mass spectrometry-based sequencing of lignin oligomers Plant Physiol. 153 2010 1464 1478
41. K. Morreel, H. Kim, F.C. Lu, O. Dima, T. Akiyama, R. Vanholme, C. Niculaes, G. Goeminne, D. Inze, E. Messens, J. Ralph, and W. Boerjan Mass spectrometry-based fragmentation as an identification tool in lignomics Anal. Chem. 82 2010 8095 8105
42. A. Moussaieff, I. Rogachev, L. Brodsky, S. Malitsky, T.W. Toal, H. Belcher, M. Yativ, S.M. Brady, P.N. Benfey, and A. Aharoni High-resolution metabolic mapping of cell types in plant roots Proc. Natl. Acad. Sci. U. S. A. 110 2013 E1232 1241
43. T. Nakatsubo, M. Mizutani, S. Suzuki, T. Hattori, and T. Umezawa Characterization of Arabidopsis thaliana pinoresinol reductase, a new type of enzyme involved in lignan biosynthesis J. Biol. Chem. 283 2008 15550 15557
44. H. Noren, P. Svensson, and B. Andersson A convenient and versatile hydroponic cultivation system for Arabidopsis thaliana Physiol. Plantarum 121 2004 343 348
45. E. Oburger, M. Dell'mour, S. Hann, G. Wieshammer, M. Puschenreiter, and W.W. Wenzel Evaluation of a novel tool for sampling root exudates from soil-grown plants compared to conventional techniques Environ. Exp. Bot. 87 2013 235 247
46. O. Olsen, and H. Sorensen Glucosinolates and amines in Reseda media Phytochemistry 19 1980 1783 1787
47. B.L. Petersen, S. Chen, C.H. Hansen, C.E. Olsen, and B.A. Halkier Composition and content of glucosinolates in developing Arabidopsis thaliana Planta 214 2002 562 571
48. T. Rudrappa, K.J. Czymmek, P.W. Pare, and H.P. Bais Root-secreted malic acid recruits beneficial soil bacteria Plant Physiol. 148 2008 1547 1556
49. B. Schlesier, F. Breton, and H.P. Mock A hydroponic culture system for growing Arabidopsis thaliana plantlets under sterile conditions Plant Mol. Biol. Rep. 21 2003 449 456
50. N.B. Schmid, R.F. Giehl, S. Doll, H.P. Mock, N. Strehmel, D. Scheel, X. Kong, R.C. Hider, and N. von Wiren Feruloyl-CoA 6'-Hydroxylase1-dependent coumarins mediate iron acquisition from alkaline substrates in Arabidopsis Plant Physiol. 164 2014 160 172
51. H. Schmidt, C. Günther, M. Weber, C. Spörlein, S. Loscher, C. Böttcher, R. Schobert, and S. Clemens Metabolome analysis of Arabidopsis thaliana roots identifies a key metabolic pathway for iron acquisition PLoS One 9 7 2014 e102444
52. M. Schreiner, A. Krumbein, D. Knorr, and I. Smetanska Enhanced glucosinolates in root exudates of Brassica rapa ssp. rapa mediated by salicylic acid and methyl jasmonate J. Agric. Food Chem. 59 2011 1400 1405
53. C.A. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal. Chem. 78 2006 779 787
54. R. Tautenhahn, C. Bottcher, and S. Neumann Highly sensitive feature detection for high resolution LC/MS BMC Bioinf. 9 2008 504
55. L. Tilstra, M.C. Sattler, W.R. Cherry, and M.D. Barkley Fluorescence of a rotationally constrained tryptophan derivative, 3-carboxy-1,2,3,4-tetrahydro-2-carboline J. Am. Chem. Soc. 112 1990 9176 9182
56. P. Tocquin, L. Corbesier, A. Havelange, A. Pieltain, E. Kurtem, G. Bernier, and C. Perilleux A novel high efficiency, low maintenance, hydroponic system for synchronous growth and flowering of Arabidopsis thaliana BMC Plant Biol. 3 2003 2
57. T. Toda, H. Koyama, and T. Hara A simple hydroponic culture method for the development of a highly viable root system in Arabidopsis thaliana Biosci. Biotechnol. Biochem. 63 1999 210 212
58. N. von Wiren, V. Romheld, T. Shioiri, and H. Marschner Competition between microorganisms and roots of barley and Sorghum for iron accumulated in the root apoplasm New Phytol. 130 1995 511 521
59. F. Wen, H.D. VanEtten, G. Tsaprailis, and M.C. Hawes Extracellular proteins in pea root tip and border cell exudates Plant Physiol. 143 2007 773 783
60. U. Wittstock, and M. Burow Glucosinolate breakdown in Arabidopsis: mechanism, regulation and biological significance Arabidopsis Book 8 2010 e0134
61. S. Yahara, N. Uda, E. Yoshio, and E. Yae Steroidal alkaloid glycosides from tomato (Lycopersicon esculentum) J. Nat. Prod. 67 2004 500 502
62. K. Yonekura-Sakakibara, T. Tohge, F. Matsuda, R. Nakabayashi, H. Takayama, R. Niida, A. Watanabe-Takahashi, E. Inoue, and K. Saito Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis Plant Cell 20 2008 2160 2176
63. K. Zhang, R. Halitschke, C. Yin, C.J. Liu, and S.S. Gan Salicylic acid 3-hydroxylase regulates Arabidopsis leaf longevity by mediating salicylic acid catabolism Proc. Natl. Acad. Sci. U. S. A. 110 2013 14807 14812
64. M. Zoeller, N. Stingl, M. Krischke, A. Fekete, F. Waller, S. Berger, and M.J. Mueller Lipid profiling of the Arabidopsis hypersensitive response reveals specific lipid peroxidation and fragmentation processes: biogenesis of pimelic and azelaic acid Plant Physiol. 160 2012 365 378