Tools for high-spatial and temporal-resolution analysis of environmental responses in plants

Biotechnology Letters

Volumn 32, Issue 10, 2010, Pages 1361-1371

  Wee, Choon W ^a   Dinneny, J R ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Biosensors; Environmental stimuli; Metabolomics; Plants; Proteomics; Salt stress; Stress; Transcriptomics; Translatome

Indexed keywords

ENVIRONMENTAL STIMULI; METABOLOMICS; PLANTS; PROTEOMICS; SALT STRESS; TRANSCRIPTOMICS; TRANSLATOME;

BIOSENSORS; CALCIUM; CROPS; HARDWOODS; MOLECULAR BIOLOGY; PROTEINS; SODIUM CHLORIDE; SUGAR (SUCROSE);

PLANTS (BOTANY);

GENE EXPRESSION PROFILING; GENETIC PROCEDURES; IMAGE PROCESSING; METABOLOMICS; METHODOLOGY; PHYSIOLOGICAL STRESS; PLANT PHYSIOLOGY; PROTEOMICS; REPORTER GENE; REVIEW; TIME;

BIOSENSING TECHNIQUES; GENE EXPRESSION PROFILING; GENES, REPORTER; IMAGE PROCESSING, COMPUTER-ASSISTED; METABOLOMICS; PLANT PHYSIOLOGICAL PHENOMENA; PROTEOMICS; STRESS, PHYSIOLOGICAL; TIME FACTORS;

ARABIDOPSIS;

EID: 77956717856     PISSN: 01415492     EISSN: 15736776     Source Type: Journal    
DOI: 10.1007/s10529-010-0307-8     Document Type: Review

References (77)

1. Amme S, Matros A, Schlesier B et al (2006) Proteome analysis of cold stress response in Arabidopsis thaliana using DIGE-technology. J Exp Bot 57: 1537-1546.
2. + antiporter in Arabidopsis. Science 285: 1256-1258.
3. Baerenfaller K, Grossmann J, Grobei MA et al (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320: 938-941.
4. Barakat A, Szick-Miranda K, Chang IF et al (2001) The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Plant Physiol 127: 398-415.
5. Baxter CJ, Redestig H, Schauer N et al (2007) The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol 143: 312-325.
6. Birnbaum K, Shasha DE, Wang JY et al (2003) A gene expression map of the Arabidopsis root. Science 302: 1956-1960.
7. Birnbaum K, Jung JW, Wang JY et al (2005) Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat Methods 2: 615-619.
8. Blumwald E (2000) Sodium transport and salt tolerance in plants. Curr Opin Cell Biol 12: 431-434.
9. Brady SM, Orlando DA, Lee JY et al (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318: 801-806.
10. Branco-Price C, Kawaguchi R, Ferreira RB et al (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot 96: 647-660.
11. Branco-Price C, Kaiser KA, Jang CJ et al (2008) Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J 56: 743-755.
12. Brooks TL, Miller ND, Spalding EP (2010) Plasticity of Arabidopsis root gravitropism throughout a multidimensional condition space quantified by automated image analysis. Plant Physiol 152: 206-216.
13. Brosche M, Vinocur B, Alatalo ER (2005) Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biol 6: R101.
14. Chaudhuri B, Hormann F, Lalonde S (2008) Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips. Plant J 56: 948-962.
15. Cicchetti G, Biernacki M, Farquharson J et al (2004) A ratiometric expressible FRET sensor for phosphoinositides displays a signal change in highly dynamic membrane structures in fibroblasts. Biochemistry 43: 1939-1949.
16. Cook D, Fowler S, Fiehn O et al (2004) A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci USA 101: 15243-15248.
17. Deuschle K, Okumoto S, Fehr M et al (2005) Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering. Protein Sci 14: 2304-2314.
18. Deuschle K, Chaudhuri B, Okumoto S et al (2006) Rapid metabolism of glucose detected with FRET glucose nanosensors in epidermal cells and intact roots of Arabidopsis RNA-silencing mutants. Plant Cell 18: 2314-2325.
19. Dinneny JR (2009) Analysis of the salt-stress response at cell-type resolution. Plant Cell Environ. doi: 10. 1111/j. 1365-3040. 2009. 02055. x.
20. Dinneny JR, Benfey PN (2009) Studying root development using a genomic approach. Annual Plant Reviews, Volume 37, Root Development Chapter 12, pp 325-351. Blackwell Publishing.
21. Dinneny JR, Long TA, Wang JY et al (2008) Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320: 942-945.
22. Dooley CT, Dore TM, Hanson GT et al (2004) Imaging dynamic redox changes in mammalian cells with green fluorescent protein indicators. J Biol Chem 279: 22284-22293.
23. Evanko DS, Haydon PG (2005) Elimination of environmental sensitivity in a cameleon FRET-based calcium sensor via replacement of the acceptor with Venus. Cell Calcium 37: 341-348.
24. Fehr M, Frommer WB, Lalonde S (2002) Visualization of maltose uptake in living yeast cells by fluorescent nanosensors. Proc Natl Acad Sci USA 99: 9846-9851.
25. Folta KM, Spalding EP (2001) Unexpected roles for cryptochrome 2 and phototropin revealed by high-resolution analysis of blue light-mediated hypocotyl growth inhibition. Plant J 26: 471-478.
26. Frommer WB, Davidson MW, Campbell RE (2009) Genetically encoded biosensors based on engineered fluorescent proteins. Chem Soc Rev 38: 2833-2841.
27. Gasch AP, Eisen MB (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 3: RESEARCH0059.
28. Gifford ML, Dean A, Gutierrez RA et al (2008) Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci USA 105: 803-808.
29. Hanson GT, Aggeler R, Oglesbee D (2004) Investigating mitochondrial redox potential with redox-sensitive green fluorescent protein indicators. J Biol Chem 279: 13044-13053.
30. Heim N, Griesbeck O (2004) Genetically encoded indicators of cellular calcium dynamics based on troponin C and green fluorescent protein. J Biol Chem 279: 14280-14286.
31. Hellwig N, Plant TD, Janson W (2004) TRPV1 acts as proton channel to induce acidification in nociceptive neurons. J Biol Chem 279: 34553-34561.
32. Hernandez G, Ramirez M, Valdes-Lopez O (2007) Phosphorus stress in common bean: root transcript and metabolic responses. Plant Physiol 144: 752-767.
33. Honda A, Adams SR, Sawyer CL (2001) Spatiotemporal dynamics of guanosine 3′, 5′-cyclic monophosphate revealed by a genetically encoded, fluorescent indicator. Proc Natl Acad Sci USA 98: 2437-2442.
34. Inoue T, Heo WD, Grimley JS et al (2005) An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways. Nat Methods 2: 415-418.
35. Iyer-Pascuzzi A, Simpson J, Herrera-Estrella L et al (2009) Functional genomics of root growth and development in Arabidopsis. Curr Opin Plant Biol 12: 165-171.
36. Jiang Y, Deyholos MK (2006) Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes. BMC Plant Biol 6: 25.
37. Jiang K, Schwarzer C, Lally E et al (2006) Expression and characterization of a redox-sensing green fluorescent protein (reduction-oxidation-sensitive green fluorescent protein) in Arabidopsis. Plant Physiol 141: 397-403.
38. Jiang Y, Yang B, Harris NS et al (2007) Comparative proteomic analysis of NaCl stress-responsive proteins in Arabidopsis roots. J Exp Bot 58: 3591-3607.
39. Jubany-Mari T, Alegre-Batlle L, Jiang K et al (2010) Use of a redox-sensing GFP (c-roGFP1) for real-time monitoring of cytosol redox status in Arabidopsis thaliana water-stressed plants. FEBS Lett 584: 889-897.
40. Jurgens G (2004) Membrane trafficking in plants. Annu Rev Cell Dev Biol 20: 481-504.
41. Kaplan F, Kopka J, Sung DY (2007) Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant J 50: 967-981.
42. Karasawa S, Araki T, Nagai T et al (2004) Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer. Biochem J 381: 307-312.
43. Kuner T, Augustine GJ (2000) A genetically encoded ratiometric indicator for chloride: capturing chloride transients in cultured hippocampal neurons. Neuron 27: 447-459.
44. Kunkel MT, Ni Q, Tsien RY et al (2005) Spatio-temporal dynamics of protein kinase B/Akt signaling revealed by a genetically encoded fluorescent reporter. J Biol Chem 280: 5581-5587.
45. Le Lay P, Isaure MP, Sarry JE et al (2006) Metabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to a caesium stress. Influence of potassium supply. Biochimie 88: 1533-1547.
46. 2-containing vesicles with tonoplast and increased salt tolerance. Proc Natl Acad Sci USA 103: 18008-18013.
47. Liscum E, Hangarter RP (1993) Light-stimulated apical hook opening in wild-type Arabidopsis thaliana seedlings. Plant Physiol 101: 567-572.
48. Looger LL, Lalonde S, Frommer WB (2005) Genetically encoded FRET sensors for visualizing metabolites with subcellular resolution in living cells. Plant Physiol 138: 555-557.
49. + imaging. J Neurosci Methods 155: 251-259.
50. Miller ND, Parks BM, Spalding EP (2007) Computer-vision analysis of seedling responses to light and gravity. Plant J 52: 374-381.
51. + transport in Arabidopsis. Plant Cell 21: 2163-2178.
52. Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59: 651-681.
53. Mustroph A, Zanetti ME, Jang CJ et al (2009) Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci USA 106: 18843-18848.
54. Nelson DE, Repetti PP, Adams TR et al (2007) Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres. Proc Natl Acad Sci USA 104: 16450-16455.
55. Nikiforova VJ, Gakiere B, Kempa S et al (2004) Towards dissecting nutrient metabolism in plants: a systems biology case study on sulphur metabolism. J Exp Bot 55: 1861-1870.
56. Oh DH, Leidi E, Zhang Q et al (2009) Loss of halophytism by interference with SOS1 expression. Plant Physiol 151: 210-222.
57. Oh DH, Lee SY, Bressan RA et al (2010) Intracellular consequences of SOS1 deficiency during salt stress. J Exp Bot 61: 1205-1213.
58. Okumoto S, Looger LL, Micheva KD et al (2005) Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors. Proc Natl Acad Sci USA 102: 8740-8745.
59. Parks BM, Folta KM, Spalding EP (2001) Photocontrol of stem growth. Curr Opin Plant Biol 4: 436-440.
60. Preiss T, Hentze MW (2003) Starting the protein synthesis machine: eukaryotic translation initiation. Bioessays 25: 1201-1211.
61. Riesmeier JW, Willmitzer L, Frommer WB (1992) Isolation and characterization of a sucrose carrier cDNA from spinach by functional expression in yeast. EMBO J 11: 4705-4713.
62. 2+-dependent changes in the fluorescence emission of an indicator composed of two green fluorescent protein variants linked by a calmodulin-binding sequence. A new class of fluorescent indicators. J Biol Chem 272: 13270-13274.
63. Sato M, Ozawa T, Inukai K et al (2002) Fluorescent indicators for imaging protein phosphorylation in single living cells. Nat Biotechnol 20: 287-294.
64. Seth A, Otomo T, Yin HL et al (2003) Rational design of genetically encoded fluorescence resonance energy transfer-based sensors of cellular Cdc42 signaling. Biochemistry 42: 3997-4008.
65. + antiporter gene improves salt tolerance in Arabidopsis thaliana. Nat Biotechnol 21: 81-85.
66. Skopelitis DS, Paranychianakis NV, Paschalidis KA et al (2006) Abiotic stress generates ROS that signal expression of anionic glutamate dehydrogenases to form glutamate for proline synthesis in tobacco and grapevine. Plant Cell 18: 2767-2781.
67. + symporter in lipid vesicles and purification of the histidine tagged protein from transgenic Saccharomyces cerevisiae. Plant J 6: 225-233.
68. Takemoto K, Nagai T, Miyawaki A et al (2003) Spatio-temporal activation of caspase revealed by indicator that is insensitive to environmental effects. J Cell Biol 160: 235-243.
69. Violin JD, Zhang J, Tsien RY et al (2003) A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C. J Cell Biol 161: 899-909.
70. Warner JR, McIntosh KB (2009) How common are extraribosomal functions of ribosomal proteins? Mol Cell 34: 3-11.
71. Widodo JH, Newbigin E, Tester M et al (2009) Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance. J Exp Bot 60: 4089-4103.
72. +- and pH-dependent manner. Proc Natl Acad Sci USA 102: 16107-16112.
73. Zaccolo M (2004) Use of chimeric fluorescent proteins and fluorescence resonance energy transfer to monitor cellular responses. Circ Res 94: 866-873.
74. Zanetti ME, Chang IF, Gong F et al (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol 138: 624-635.
75. Zeller G, Henz SR, Widmer CK et al (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J 58: 1068-1082.
76. Zhou Y, Qu H, Dibley KE et al (2007) A suite of sucrose transporters expressed in coats of developing legume seeds includes novel pH-independent facilitators. Plant J 49: 750-764.
77. Zhu H, Bilgin M, Snyder M (2003) Proteomics. Annu Rev Biochem 72: 783-812.