Metabolomics integrated with transcriptomics: Assessing systems response to sulfur-deficiency stress

Physiologia Plantarum

Volumn 132, Issue 2, 2008, Pages 190-198

  Hoefgen, Rainer ^a   Nikiforova, Victoria J ^a,b  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b TIMIRYAZEV INSTITUTE OF PLANT PHYSIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

SULFUR;

BIOLOGY; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; PLANT; REVIEW;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; PLANTS; SULFUR;

ANIMALIA; ARABIDOPSIS;

EID: 38149062772     PISSN: 00319317     EISSN: 13993054     Source Type: Journal    
DOI: 10.1111/j.1399-3054.2007.01012.x     Document Type: Review

References (50)

1. Askenazi M, Driggers EM, Holtzman DA, Norman TC, Iverson S, Zimmer DP, Boers ME, Blomquist PR, Martinez EJ, Monreal AW, Feibelman TP, Mayorga ME, Maxon ME, Sykes K, Tobin JV, Cordero E, Salama SR, Trueheart J, Royer JC, Madden KT (2003) Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat Biotechnol 21 : 150 156
2. Barlier I, Kowalczyk M, Marchant A, Ljung K, Bhalerao R, Bennett M, Sandberg G, Bellini C (2000) The SUR2 gene of Arabidopsis thaliana encodes the cytochrome P450 CYP83B1, a modulator of auxin homeostasis. Proc Natl Acad Sci USA 97 : 14819 14824
3. Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9 : 418 425
4. Blake-Kalff MMA, Harrison KR, Hawkesford MJ, Zhao FJ, McGrath SP (1998) Distribution of sulfur within oilseed rape leaves in response to sulfur deficiency during vegetative growth. Plant Physiol 118 : 1337 1344
5. Bones AM, Rossiter JT (1996) The myrosinase-glucosinolate system, its organisation and biochemistry. Physiol Plant 97 : 194 208
6. Bylesjö M, Eriksson D, Kusano M, Moritz T, Trygg J (2007) Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. The Plant J doi:10.1111/j.1365-313X.2007.03293.x
7. Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor M-I, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M, Sweetlove L, Fernie AR (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behaviour. Plant Physiol 142 : 1380 1396
8. Casimiro I, Beeckman T, Graham N, Bhalerao R, Zhang H, Casero P, Sandberg G, Bennett MJ (2003) Dissecting Arabidopsis lateral root development. Trends Plant Sci 8 : 165 171
9. Clarkson DT, Diogo E, Amancio S (1999) Uptake and assimilation of sulphate by sulphur deficient Zea mays cells: the role of O-acetyl-L-serine in the interaction between nitrogen and sulphur assimilatory pathways. Plant Physiol Biochem 37 : 283 290
10. Colebatch G, Desbrosses G, Ott T, Krusell L, Montanari O, Kloska S, Kopka J, Udvardi MK (2004) Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant J 39 : 487 512
11. Dan H, Yang GH, Zheng ZL (2007) A negative regulatory role for auxin in sulphate deficiency response in Arabidopsis thaliana. Plant Mol Biol 63 : 221 235
12. Ernest S, Carter M, Shao HF, Hosack A, Lerner N, Colmenares C, Rosenblatt DS, Pao YH, Ross ME, Nadeau JH (2006) Parallel changes in metabolite and expression profiles in crooked-tail mutant and folate-reduced wild-type mice. Human Mol Genet 15 : 3387 3393
13. Fernie AR, Urbanczyk-Wochniak E, Willmitzer L (2005) Parallel metabolite and transcript profiling - hypothesis generation for biotechnology. In : Vaidyanathan S, Harrigan GG, Goodacre R (eds) Metabolome Analyses: Strategies for Systems Biology. Springer, New York, pp 291 306
14. Halkier BA, Gershenzon J (2006) Biology and biochemistry of glucosinolates. Annu Rev Plant Biol 57 : 303 333
15. Hall R, Beale MH, Fiehn O, Hardy N, Sumner N, Bino R (2002) Plant metabolomics: the missing link in functional genomics strategies. Plant Cell 14 : 1437 1440
16. Hawkesford AJ, Buchner P, Howarth JR, Lu C (2005) Understanding the regulation of sulfur nutrition - from sulfate transporter genes to the field. Phyton 45 : 57 67
17. Higashi Y, Hirai MY, Fujiwara T, Naito S, Noji M, Saito K (2006) Proteomic and transcriptomic analysis of Arabidopsis seeds: molecular evidence for successive processing of seed proteins and its implication in the stress response to sulfur nutrition. Plant J 48 : 557 571
18. Hirai MY, Saito K (2004) Post-genomics approaches for the elucidation of plant adaptive mechanisms to sulphur deficiency. J Exp Bot 55 : 1871 1879
19. Hirai MY, Kim H, Hayashi H, Chino M, Naito S, Fujiwara T (2002) Independent roles of methionine and O-acetyl-L-serine in the regulation of the beta subunit gene of beta-conglycinin. Soil Sci Plant Nutri 48 : 87 94
20. Hirai MY, Fujiwara T, Awazuhara M, Kimura T, Noji M, Saito K (2003) Global expression profiling of sulfur-starved Arabidopsis by DNA macroarray reveals the role of O-acetyl-L-serine as a general regulator of gene expression in response to sulfur nutrition. Plant J 33 : 651 663
21. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci USA 101 : 10205 10210
22. Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280 : 25590 25595
23. Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Araki R, Sakurai N, Suzuki H, Aoki K, Goda H, Nishizawa OI, Shibata D, Saito K (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci USA 104 : 6478 6483
24. Hopkins L, Parmar S, Baszczyk A, Hesse H, Hoefgen R, Hawkesford MJ (2005) O-acetylserine and the regulation of expression of genes encoding components for sulfate uptake and assimilation in potato. Plant Physiol 138 : 433 440
25. Kim H, Hirai MY, Hayashi H, Chino M, Naito S, Fujiwara T (1999) Role of O-acetyl-L-serine in the coordinated regulation of the expression of a soybean seed storage-protein gene by sulfur and nitrogen nutrition. Planta 209 : 282 289
26. Kolbe A, Oliver SN, Fernie AR, Stitt M, van Dongen JT, Geigenberger P (2006) Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism. Plant Physiol 141 : 412 422
27. Kopka J, Fernie A, Weckwerth W, Gibon Y, Stitt M (2004) Metabolite profiling in plant biology: platforms and destinations. Genome Biol 5 : 109
28. Koza RA, Herbst EJ (1992) Deficiencies in DNA replication and cell-cycle progression in polyamine-depleted HeLa cells. Biochem J 281 : 87 93
29. Kutz A, Muller A, Hennig P, Kaiser WM, Piotrowski M, Weiler EW (2002) A role for nitrilase 3 in the regulation of root morphology in sulphur-starving Arabidopsis thaliana. Plant J 30 : 95 106
30. Lafaye A, Junot C, Pereira Y, Lagniel G, Tabet JC, Ezan E, Labarre J (2005) Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism. J Biol Chem 280 : 24723 24730
31. Lappartient AG, Vidmar JJ, Leustek T, Glass ADM, Touraine B (1999) Inter organ signaling in plants: regulation of ATP sulfurylase and sulfate transporter genes expression in roots mediated by phloem-translocated compounds. Plant J 18 : 89 95
32. Lopez-Bucio J, Cruz-Ramirez A, Herrera-Estrella L (2003) The role of nutrient availability in regulating root architecture. Curr Opin Plant Biol 6 : 280 287
33. Malamy JE, Ryan KS (2001) Environmental regulation of lateral root initiation in Arabidopsis. Plant Physiol 127 : 899 909
34. Morgan DM (1999) Polyamines. An overview. Mol Biotechnol 11 : 229 250
35. Nikiforova V, Freitag J, Kempa S, Adamik M, Hesse H, Hoefgen R (2003) Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. Plant J 33 : 633 650
36. Nikiforova V, Gakière B, Kempa S, Adamik M, Willmitzer L, Hesse H, Hoefgen R (2004) Towards dissecting nutrient metabolism in plants: a systems biology case study on sulfur metabolism. J Exp Bot 55 : 1861 1870
37. Nikiforova VJ, Kopka J, Tolstikov V, Fiehn O, Hopkins L, Hawkesford MJ, Hesse H, Hoefgen R (2005a) Systems re-balancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiol 138 : 304 318
38. Nikiforova VJ, Daub CO, Hesse H, Willmitzer L, Hoefgen R (2005b) Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. J Exp Bot 56 : 1887 1896
39. Osuna D, Usadel B, Morcuende R, Gibon Y, Blasing OE, Hohne M, Gunter M, Kamlage B, Trethewey R, Scheible WR, Stitt M (2007) Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J 49 : 463 491
40. Rask L, Andreasson E, Ekbom B, Eriksson S, Pontoppidan B, Meijer J (2000) Myrosinase: gene family evolution and herbivore defense in Brassicaceae. Plant Mol Biol 42 : 93 113
41. Rogg LE, Lasswell J, Bartel B (2001) A gain-of-function mutation in IAA28 suppresses lateral root development. Plant Cell 13 : 465 480
42. Schauer N, Fernie AR (2006) Plant metabolomics: towards biological function and mechanism. Trends Plant Sci 11 : 508 516
43. Scheible WR, Morcuende R, Czechowski T, Fritz C, Osuna D, Palacios-Rojas N, Schindelasch D, Thimm O, Udvardi MK, Stitt M (2004) Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol 136 : 2483 2499
44. Steinhauser D, Kopka J (2007) Methods, applications and concepts of metabolite profiling: primary metabolism. In : Baginsky S, Fernie AR (eds) Plant Systems Biology. Birkhäuser, Heidelberg, pp 171 194
45. Szymanski J, Adamik M, Carrari F, Fernie AR, Hoefgen R, Nikiforova VJ (2007) On the processing of metabolic information through metabolite-gene communication networks: an approach for modelling causality. Phytochem 68 : 2163 2175
46. Tabib A, Bachrach U (1994) Activation of the proto-oncogene c-myc and c-fos by c-ras: involvement of polyamines. Biochem Biophys Res Commun 202 : 720 727
47. Urbanczyk-Wochniak E, Luedemann A, Kopka J, Selbig J, Roessner-Tunali U, Willmitzer L, Fernie AR (2003) Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep 4 : 989 993
48. Urbanczyk-Wochniak E, Baxter C, Kolbe A, Kopka J, Sweetlove LJ, Fernie AR (2005) Profiling of diurnal patterns of metabolite and transcript abundance in potato (Solanum tuberosum) leaves. Planta 221 : 891 903
49. Zazimalova E, Napier RM (2003) Points of regulation for auxin action. Plant Cell Rep 21 : 625 634
50. Zhao F, Evans EJ, Bilsborrow PE, Syers JK (1994) Influence of nitrogen and sulphur on the glucosinolate profile of rapeseed (Brassica napus L.). J Sci Food Agric 64 : 295 304