Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Monchgesang, Susann ^a   Strehmel, Nadine ^a   Schmidt, Stephan ^a   Westphal, Lore ^a   Taruttis, Franziska ^a,b   Muller, Erik ^a   Herklotz, Siska ^a   Neumann, Steffen ^a   Scheel, Dierk ^a  

^a LEIBNIZ INSTITUTE OF PLANT BIOCHEMISTRY   (Germany)

^b UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COUMARIC ACID; GLUCOSINOLATE;

ANALYSIS; ARABIDOPSIS; CHEMISTRY; CLUSTER ANALYSIS; ELECTROSPRAY MASS SPECTROMETRY; GENETIC VARIATION; GENETICS; GENOMICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROLYSIS; METABOLISM; METABOLOME; METABOLOMICS; PLANT EXUDATE; PLANT ROOT; RHIZOSPHERE;

ARABIDOPSIS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CLUSTER ANALYSIS; COUMARIC ACIDS; GENETIC VARIATION; GENOMICS; GLUCOSINOLATES; HYDROLYSIS; METABOLOME; METABOLOMICS; PLANT EXUDATES; PLANT ROOTS; RHIZOSPHERE; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 84976866457     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep29033     Document Type: Article

References (47)

1. Weigel, D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 158, 2-22 (2012).
2. Mithen, R., Clarke, J. H., Lister, C., Dean, C. Genetics of aliphatic glucosinolates. III. Side chain structure of aliphatic glucosinolates in Arabidopsis thaliana. Heredity (Edinb). 74, 210-215 (1995).
3. Mithen, R., Campos, H. Genetic variation of aliphatic glucosinolates in Arabidopsis thaliana and prospects for map based gene cloning. Entomologica Experimentalis et Applicanta. 53, 202-205 (1996).
4. Magrath, R. et al. Genetics of aliphatic glucosinolates. I. Side chain elongation in Brassica napus and Arabidopsis thaliana. Heredity (Edinb). 72, 290-299 (1994).
5. Mitchell-Olds, T., Pedersen, D. The molecular basis of quantitative genetic variation in central and secondary metabolism in Arabidopsis. Genetics. 149, 739-747 (1998).
6. Kliebenstein, D. J. et al. Genetic control of natural variation in Arabidopsis glucosinolate accumulation. Plant Physiol. 126, 811-825 (2001).
7. Houshyani, B. et al. Characterization of the natural variation in Arabidopsis thaliana metabolome by the analysis of metabolic distance. Metabolomics. 8, 131-145 (2012).
8. Agrawal, B., Lakshmanan, V., Kaushik, S., Bais, H. P. Natural variation among Arabidopsis accessions reveals malic acid as a key mediator of Nickel (Ni) tolerance. Planta. 236, 477-489 (2012).
9. Bais, H. P., Weir, T. L., Perry, L. G., Gilroy, S., Vivanco, J. M. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol. 57, 233-266 (2006).
10. Schmid, N. B. et al. Feruloyl-CoA 6?-Hydroxylase1-dependent coumarins mediate iron acquisition from alkaline substrates in Arabidopsis. Plant Physiol. 164, 160-172 (2014).
11. van de Mortel, J. E. et al. Metabolic and transcriptomic changes induced in Arabidopsis by the rhizobacterium Pseudomonas fluorescens SS101. Plant Physiol. 160, 2173-2188 (2012).
12. Hiltner, L. Über neue Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie. Arbeiten der Deutschen Landwirtschaft Gesellschaft. 98, 59-78 (1904).
13. Bulgarelli, D., Schlaeppi, K., Spaepen, S., Ver Loren van Themaat, E., Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol. 64, 807-838 (2013).
14. Bressan, M. et al. Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J. 3, 1243-1257 (2009).
15. Strehmel, N., Böttcher, C., Schmidt, S., Scheel, D. Profiling of secondary metabolites in root exudates of Arabidopsis thaliana. Phytochemistry. 108C, 35-46 (2014).
16. Micallef, S. A., Shiaris, M. P., Colon-Carmona, A. Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot. 60, 1729-1742 (2009).
17. Böttcher, C., von Roepenack-Lahaye, E., Scheel, D. Resources for metabolomics in Genetics and Genomics of the Brassicaceae Vol. 9 Plant Genetics and Genomics: Crops and Models (eds Bancroft, I., Schmidt, R.) 469-503 (Springer, 2011).
18. Kover, P. X. et al. A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet. 5, e1000551 (2009).
19. Nordborg, M. et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3, e196 (2005).
20. Clark, R. M. et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science. 317, 338-342 (2007).
21. Editorial. How robust are your data? Nature Cell Biology. 11 (2009).
22. Gan, X. et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 477, 419-423 (2011).
23. Wiesner, M., Schreiner, M., Zrenner, R. Functional identification of genes responsible for the biosynthesis of 1-methoxy-indol-3-ylmethyl-glucosinolate in Brassica rapa ssp. chinensis. BMC Plant Biol. 14, 124 (2014).
24. Pfalz, M. et al. Metabolic engineering in Nicotiana benthamiana reveals key enzyme functions in Arabidopsis indole glucosinolate modification. Plant Cell. 23, 716-729 (2011).
25. Keurentjes, J. J. et al. The genetics of plant metabolism. Nat Genet. 38, 842-849 (2006).
26. Obayashi, T. et al. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res. 35, D863-869 (2007).
27. De Pessemier, J., Chardon, F., Juraniec, M., Delaplace, P., Hermans, C. Natural variation of the root morphological response to nitrate supply in Arabidopsis thaliana. Mech Dev. 130, 45-53 (2013).
28. Trontin, C., Tisne, S., Bach, L., Loudet, O. What does Arabidopsis natural variation teach us (and does not teach us) about adaptation in plants? Curr Opin Plant Biol. 14, 225-231 (2011).
29. Ziegler, J. et al. Simultaneous analysis of apolar phytohormones and 1-aminocyclopropan-1-carboxylic acid by high performance liquid chromatography/electrospray negative ion tandem mass spectrometry via 9-fluorenylmethoxycarbonyl chloride derivatization. J Chromatogr A. 1362, 102-109 (2014).
30. Li, X. et al. Exploiting natural variation of secondary metabolism identifies a gene controlling the glycosylation diversity of dihydroxybenzoic acids in Arabidopsis thaliana. Genetics. 198, 1267-1276 (2014).
31. Negishi, M. et al. Structure and function of sulfotransferases. Arch Biochem Biophys. 390, 149-157 (2001).
32. Stracke, R. et al. Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J. 50, 660-677 (2007).
33. Jones, P., Messner, B., Nakajima, J., Schaffner, A. R., Saito, K. UGT73C6 and UGT78D1, glycosyltransferases involved in flavonol glycoside biosynthesis in Arabidopsis thaliana. J Biol Chem. 278, 43910-43918 (2003).
34. Tautenhahn, R., Böttcher, C., Neumann, S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics. 9, 504 (2008).
35. Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., Siuzdak, G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 78, 779-787 (2006).
36. Böttcher, C. et al. The multifunctional enzyme CYP71B15 (PHYTOALEXIN DEFICIENT3) converts cysteine-indole-3-acetonitrile to camalexin in the indole-3-acetonitrile metabolic network of Arabidopsis thaliana. Plant Cell. 21, 1830-1845 (2009).
37. Benjamini, Y., Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J. R. Stat. Soc. B 57, 289-300 (1995).
38. R: A Language and Environment for Statistical Computing (2014).
39. Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
40. Leek, J. T., Storey, J. D. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3, 1724-1735 (2007).
41. Suzuki, R., Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 22, 1540-1542 (2006).
42. BSgenome.Athaliana.TAIR.TAIR9: Full genome sequences for Arabidopsis thaliana (TAIR9).
43. Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 9, e1003118 (2013).
44. Kuhl, C., Tautenhahn, R., Böttcher, C., Larson, T. R., Neumann, S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem. 84, 283-289 (2012).
45. Mueller, L. A., Zhang, P., Rhee, S. Y. AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol. 132, 453-460 (2003).
46. Huala, E. et al. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 29, 102-105 (2001).
47. Luo, J. et al. A novel polyamine acyltransferase responsible for the accumulation of spermidine conjugates in Arabidopsis seed. Plant Cell. 21, 318-333 (2009).