Oxidative stress components explored in anoxic and hypoxic global gene expression data

Plant Cell Monographs

Volumn 21, Issue , 2014, Pages 19-39

  Blokhina, Olga B ^a   Törönen, Petri ^b   Fagerstedt, Kurt V ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84923392191     PISSN: 18611370     EISSN: 18611362     Source Type: Book Series    
DOI: 10.1007/978-3-7091-1254-0_2     Document Type: Article

References (102)

1. Asif M, Trivedi P, Misra P, Nath P (2009) Prolyl-4-hydroxylase (AtP4H1) mediates and mimics low oxygen response in Arabidopsis thaliana. Funct Integr Genomics 9:525–535
2. Bailey-Serres J, Chang R (2005) Sensing and signalling in response to oxygen deprivation in plants and other organisms. Ann Bot (Lond) 96:507–518
3. Bailey-Serres J, Voesenek LACJ (2008) Flooding stress: acclimations and genetic diversity. Annu Rev Plant Biol 59:313–339
4. Banti V, Mafessoni F, Loreti E, Alpi A, Perata P (2010) The heat-inducible transcription factor HsfA2 enhances anoxia tolerance in Arabidopsis. Plant Physiol 152:1471–1483
5. Baxter CJ, Redestig H, Schauer N, Repsilber D, Patil KR, Nielsen J, Selbig J, Liu J, Fernie AR, Sweetlove LJ (2007) The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol 143:312–325
6. Baxter-Burrell A, Yang Z, Springer PS, Bailey-Serres J (2002) RopGAP4-dependent Rop GTPase rheostat control of Arabidopsis oxygen deprivation tolerance. Science 296:2026–2028
7. Benamar A, Rolletschek H, Borisjuk L, Avelange-Macherel M, Curien G, Mostefai HA, Andriantsitohaina R, Macherel D (2008) Nitrite–nitric oxide control of mitochondrial respiration at the frontier of anoxia. Biochim Biophys Acta—Bioenergetics 1777:1268–1275
8. Berra E, Ginouves A, Pouyssegur J (2006) The hypoxia-inducible-factor hydroxylases bring fresh air into hypoxia signalling. EMBO Rep 7:41–45
9. Biemelt S, Keetman U, Albrecht G (1998) Re-aeration following hypoxia or anoxia leads to activation of the antioxidative defense system in roots of wheat seedlings. Plant Physiol 116:651–658
10. Biemelt S, Keetman U, Mock H, Grimm B (2000) Expression and activity of isoenzymes of superoxide dismutase in wheat roots in response to hypoxia and anoxia. Plant Cell Environ 23:135–144
11. Blokhina O, Fagerstedt KV (2010a) Oxidative metabolism, ROS and NO under oxygen deprivation. Plant Physiol Biochem 48:359–373
12. Blokhina O, Fagerstedt KV (2010b) Reactive oxygen species and nitric oxide in plant mitochondria: origin and redundant regulatory systems. Physiol Plant 138:447–462
13. Blokhina OB, Virolainen E, Fagerstedt KV, Hoikkala A, Wähälä K, Chirkova TV (2000) Antioxidant status of anoxia-tolerant and -intolerant plant species under anoxia and reaeration. Physiol Plant 109:396–403
14. Blokhina OB, Chirkova TV, Fagerstedt KV (2001) Anoxic stress leads to hydrogen peroxide formation in plant cells. J Exp Bot 52:1179–1190
15. Blokhina O, Virolainen E, Fagerstedt KV (2003) Antioxidants, oxidative damage and oxygen deprivation stress: a review. Ann Bot (Lond) 91:179–194
16. Blomster T, Salojärvi J, Sipari N, Brosché M, Ahlfors R, Keinänen M, Overmyer K, Kangasjärvi J (2011) Apoplastic reactive oxygen species transiently decrease auxin signaling and cause stress-induced morphogenic response in Arabidopsis. Plant Physiol 157:1866–1883
17. Borisjuk L, Macherel D, Benamar A, Wobus U, Rolletschek H (2007) Low oxygen sensing and balancing in plant seeds: a role for nitric oxide. New Phytol 176:813–823
18. Bouché N, Fait A, Bouchez D, Møller SG, Fromm H (2003) Mitochondrial succinic-semialdehyde dehydrogenase of the γ-aminobutyrate shunt is required to restrict levels of reactive oxygen intermediates in plants. Proc Natl Acad Sci U S A 100:6843–6848
19. Branco-Price C, Kawaguchi R, Ferreira RB, Bailey-Serres J (2005) Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot (Lond) 96:647–660
20. Branco-Price C, Kaiser KA, Jang CJH, Larive CK, Bailey-Serres J (2008) Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J 56:743–755
21. Brosnan JT, Brosnan ME (2006) The sulfur-containing amino acids: an overview. J Nutr 136:1636S–1640S
22. Cela J, Falk J, Munné-Bosch S (2009) Ethylene signaling may be involved in the regulation of tocopherol biosynthesis in Arabidopsis thaliana. FEBS Lett 583:992–996
23. Chang R, Jang C, Branco-Price C, Nghiem P, Bailey-Serres J (2012) Transient MPK6 activation in response to oxygen deprivation and reoxygenation is mediated by mitochondria and aids seedling survival in Arabidopsis. Plant Mol Biol 78:109–122
24. Dasgupta K, Ganesan S, Manivasagam S, Ayre B (2011) A cytochrome P450 monooxygenase commonly used for negative selection in transgenic plants causes growth anomalies by disrupting brassinosteroid signaling. BMC Plant Biol 11:67
25. Dordas C (2009) Nonsymbiotic hemoglobins and stress tolerance in plants. Plant Sci 176:433–440
26. Dordas C, Rivoal J, Hill RD (2003) Plant haemoglobins, nitric oxide and hypoxic stress. Ann Bot (Lond) 91:173–178
27. Ederli L, Morettini R, Borgogni A, Wasternack C, Miersch O, Reale L, Ferranti F, Tosti N, Pasqualini S (2006) Interaction between nitric oxide and ethylene in the induction of alternative oxidase in ozone-treated tobacco plants. Plant Physiol 142:595–608
28. Efron B, Tibshirani R (2007) On testing the significance of sets of genes. Ann Appl Stat 1:107–129
29. Fait A, Yellin A, Fromm H (2005) GABA shunt deficiencies and accumulation of reactive oxygen intermediates: insight from Arabidopsis mutants. FEBS Lett 579:415–420
30. Fait A, Fromm H, Walter D, Galili G, Fernie AR (2008) Highway or byway: the metabolic role of the GABA shunt in plants. Trends Plant Sci 13:14–19
31. Fukao T, Bailey-Serres J (2004) Plant responses to hypoxia—is survival a balancing act? Trends Plant Sci 9:449–456
32. Fukao T, Bailey-Serres J (2008) Ethylene—a key regulator of submergence responses in rice. Plant Sci 175:43–51
33. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80
34. Gonzali S, Loreti E, Novi G, Poggi A, Alpi A, Perata P (2005) The use of microarrays to study the anaerobic response in Arabidopsis. Ann Bot (Lond) 96:661–668
35. Greenway H, Gibbs J (2003) Review: mechanisms of anoxia tolerance in plants. II. Energy requirements for maintenance and energy distribution to essential processes. Funct Plant Biol 30:999–1036
36. Gupta KJ, Zabalza A, van Dongen JT (2009) Regulation of respiration when the oxygen availability changes. Physiol Plant 137:383–391
37. Gupta KJ, Igamberdiev AU, Manjunatha G, Segu S, Moran JF, Neelawarne B, Bauwe H, Kaiser WM (2011a) The emerging roles of nitric oxide (NO) in plant mitochondria. Plant Sci 181:520–526
38. Gupta KJ, Hebelstrup KH, Mur LAJ, Igamberdiev AU (2011b) Plant hemoglobins: important players at the crossroads between oxygen and nitric oxide. FEBS Lett 585:3843–3849
39. Gupta KJ, Shah JK, Brotman Y, Jahnke K, Willmitzer L, Kaiser WM, Bauwe H, Igamberdiev AU (2012) Inhibition of aconitase by nitric oxide leads to induction of the alternative oxidase and to a shift of metabolism towards biosynthesis of amino acids. J Exp Bot 63:1773–1784
40. Hebelstrup KH, Igamberdiev AU, Hill RD (2007) Metabolic effects of hemoglobin gene expression in plants. Gene 398:86–93
41. Hebelstrup KH, van Zanten M, Mandon J, Voesenek LACJ, Harren FJM, Cristescu SM, Møller IM, Mur LAJ (2012) Haemoglobin modulates NO emission and hyponasty under hypoxiarelated stress in Arabidopsis thaliana. J Exp Bot 63:5581–5591
42. Hill RD (2012) Non-symbiotic haemoglobins—what’s happening beyond nitric oxide scavenging? AoB Plants 2012:pls004
43. Hoffman DL, Salter JD, Brookes PS (2007) Response of mitochondrial reactive oxygen species generation to steady-state oxygen tension: implications for hypoxic cell signaling. Am J Physiol Heart Circ Physiol 292:H101–H108
44. Huang S, Colmer TD, Millar AH (2008) Does anoxia tolerance involve altering the energy currency towards PPi? Trends Plant Sci 13:221–227
45. Hughes RK, De Domenico S, Santino A (2009) Plant cytochrome CYP74 family: biochemical features, endocellular localisation, activation mechanism in plant defence and improvements for industrial applications. ChemBioChem 10:1122–1133
46. Huxtable RJ (1992) Physiological actions of taurine. Physiol Rev 72:101–163
47. Igamberdiev AU, Hill RD (2009) Plant mitochondrial function during anaerobiosis. Ann Bot (Lond) 103:259–268
48. Igamberdiev AU, Baron K, Manac’h-Little N, Stoimenova M, Hill RD (2005) The haemoglobin/ nitric oxide cycle: involvement in flooding stress and effects on hormone signalling [Review]. Ann Bot (Lond) 96:557–564
49. Igamberdiev AU, Bykova NV, Hill RD (2006) Nitric oxide scavenging by barley hemoglobin is facilitated by a monodehydroascorbate reductase-mediated ascorbate reduction of methemoglobin. Planta 223:1033–1040
50. Igamberdiev AU, Bykova NV, Shah JK, Hill RD (2010) Anoxic nitric oxide cycling in plants: participating reactions and possible mechanisms. Physiol Plant 138:393–404
51. Inzé A, Vanderauwera S, Hoeberichts FA, vanDorpe M, van Gaever T, van Breusegem F (2012) A subcellular localization compendium of hydrogen peroxide-induced proteins. Plant Cell Environ 35:308–320
52. Jaspers P, Kangasjärvi J (2010) Reactive oxygen species in abiotic stress signaling. Physiol Plant 138(4):405–413
53. Johnson WE, Li C, Rabinovic A (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8:118–127
54. Kataoka H, Ohnishi N (1986) Occurrence of taurine in plants. Agric Biol Chem 50(7):1887–1888
55. Lasanthi-Kudahettige R, Magneschi L, Loreti E, Gonzali S, Licausi F, Novi G, Beretta O, Vitulli F, Alpi A, Perata P (2007) Transcript profiling of the anoxic rice coleoptile. Plant Physiol 144:218–231
56. Lee SC, Mustroph A, Sasidharan R, Vashisht D, Pedersen O, Oosumi T, Voesenek LACJ, Bailey- Serres J (2011) Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia. New Phytol 190:457–471
57. Lewis DFV (2002) Oxidative stress: the role of cytochromes P450 in oxygen activation. J Chem Technol Biotechnol 77:1095–1100
58. Li C, Chen Q, Gao X, Qi B, Chen N, Xu S, Chen J, Wang X (2005) AtHsfA2 modulates expression of stress responsive genes and enhances tolerance to heat and oxidative stress in Arabidopsis. Sci China C Life Sci 48:540–550
59. Licausi F (2011) Regulation of the molecular response to oxygen limitations in plants. New Phytol 190:550–555
60. Licausi F, Van Dongen JT, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P (2010) HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J 62:302–315
61. Lindermayr C, Saalbach G, Bahnweg G, Durner J (2006) Differential inhibition of Arabidopsis methionine adenosyltransferases by protein S-nitrosylation. J Biol Chem 281:4285–4291
62. Loenarz C, Schofield CJ (2008) Expanding chemical biology of 2-oxoglutarate oxygenases. Nat Chem Biol 4:152–156
63. Loreti E, Poggi A, Novi G, Alpi A, Perata P (2005) A genome-wide analysis of the effects of sucrose on gene expression in Arabidopsis seedlings under anoxia. Plant Physiol 137:1130–1138
64. Luhua S, Ciftci-Yilmaz S, Harper J, Cushman J, Mittler R (2008) Enhanced tolerance to oxidative stress in transgenic Arabidopsis plants expressing proteins of unknown function. Plant Physiol 148:280–292
65. Manac’h-Little N, Igamberdiev AU, Hill RD (2005) Hemoglobin expression affects ethylene production in maize cell cultures. Plant Physiol Biochem 43:485–489
66. Mittler R, Vanderauwera S, Gollery M, Van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9:490–498
67. Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, Bailey-Serres J (2010) Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiol 152:1484–1500
68. Narsai R, Rocha M, Geigenberger P, Whelan J, van Dongen JT (2011) Comparative analysis between plant species of transcriptional and metabolic responses to hypoxia. New Phytol 190 (2):472–487
69. Navarre DA, Wendehenne D, Durner J, Noad R, Klessig DF (2000) Nitric oxide modulates the activity of tobacco aconitase. Plant Physiol 122:573–582
70. Navrot N, Rouhier N, Gelhaye E, Jacquot J (2007) Reactive oxygen species generation and antioxidant systems in plant mitochondria. Physiol Plant 129:185–195
71. Nelson D, Werck-Reichhart D (2011) A P450-centric view of plant evolution. Plant J 66:194–211
72. Newton MA, Quintana FA, den Boon JA, Sengupta S, Ahlquist P (2007) Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. Ann Appl Stat 1:85–106
73. Obata T, Matthes A, Koszior S, Lehmann M, Arau´jo WL, Bock R, Sweetlove LJ, Fernie AR (2011) Alteration of mitochondrial protein complexes in relation to metabolic regulation under short-term oxidative stress in Arabidopsis seedlings. Phytochemistry 72:1081–1091
74. Petrov VD, Van Breusegem F (2012) Hydrogen peroxide—a central hub for information flow in plant cells. AoB Plants 2012:pls014
75. Planchet E, Jagadis Gupta K, Sonoda M, Kaiser WM (2005) Nitric oxide emission from tobacco leaves and cell suspensions: rate limiting factors and evidence for the involvement of mitochondrial electron transport. Plant J 41:732–743
76. Potters G, Pasternak TP, Guisez Y, Jansen MAK (2009) Different stresses, similar morphogenic responses: integrating a plethora of pathways. Plant Cell Environ 32:158–169
77. Pucciariello C, Parlanti S, Banti V, Novi G, Perata P (2012) Reactive oxygen species-driven transcription in Arabidopsis under oxygen deprivation. Plant Physiol 159:184–196
78. Qiao W, Fan L (2008) Nitric oxide signaling in plant responses to abiotic stresses. J Integr Plant Biol 50:1238–1246
79. Qu Z, Zhong N, Wang H, Chen A, Jian G, Xia G (2006) Ectopic expression of the cotton non-symbiotic hemoglobin gene GhHbd1 triggers defense responses and increases disease tolerance in Arabidopsis. Plant Cell Physiol 47:1058–1068
80. Rhoads DM, Umbach AL, Subbaiah CC, Siedow JN (2006) Mitochondrial reactive oxygen species. Contribution to oxidative stress and interorganellar signaling. Plant Physiol 141:357–366
81. Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK (2007) A comparison of background correction methods for two-colour microarrays. Bioinformatics 23:2700–2707
82. Rocha M, Licausi F, Araujo WL, Nunes-Nesi A, Sodek L, Fernie AR, van Dongen JT (2010) Glycolysis and the tricarboxylic acid cycle are linked by alanine aminotransferase during hypoxia induced by waterlogging of Lotus japonicus. Plant Physiol 152:1501–1513
83. Sairam R, Kumutha D, Ezhilmathi K, Deshmukh P, Srivastava G (2008) Physiology and biochemistry of waterlogging tolerance in plants. Biol Plant 52:401–412
84. Sakamoto A, Sakurao S, Fukunaga K, Matsubara T, Ueda-Hashimoto M, Tsukamoto S, Takahashi M, Morikawa H (2004) Three distinct Arabidopsis hemoglobins exhibit peroxidase-like activity and differentially mediate nitrite-dependent protein nitration. FEBS Lett 572:27–32
85. Santosa I, Ram P, Boamfa E, Laarhoven L, Reuss J, Jackson M, Harren F (2007) Patterns of peroxidative ethane emission from submerged rice seedlings indicate that damage from reactive oxygen species takes place during submergence and is not necessarily a post-anoxic phenomenon. Planta 226:193–202
86. Shimoda Y, Nagata M, Suzuki A, Abe M, Sato S, Kato T, Tabata S, Higashi S, Uchiumi T (2005) Symbiotic rhizobium and nitric oxide induce gene expression of non-symbiotic hemoglobin in Lotus japonicus. Plant Cell Physiol 46:99–107
87. Smyth GK (2005) LIMMA: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions Using R and Bioconductor; Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (eds) Springer, New York, pp 397–420
88. Stoimenova M, Igamberdiev AU, Gupta K, Hill RD (2007) Nitrite-driven anaerobic ATP synthesis in barley and rice root mitochondria. Planta 226:465–474
89. St-Pierre J, Brand MD, Boutilier RG (2000) Mitochondria as ATP consumers: cellular treason in anoxia. Proc Natl Acad Sci U S A 97:8670–8674
90. Sweetlove LJ, Beard KFM, Nunes-Nesi A, Fernie AR, Ratcliffe RG (2010) Not just a circle: flux modes in the plant TCA cycle. Trends Plant Sci 15:462–470
91. Törönen P, Ojala P, Marttinen P, Holm L (2009) Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinformatics 10:307
92. Trevaskis B, Watts RA, Andersson CR, Llewellyn DJ, Hargrove MS, Olson JS, Dennis ES, Peacock WJ (1997) Two hemoglobin genes in Arabidopsis thaliana: the evolutionary origins of leghemoglobins. Proc Natl Acad Sci U S A 94:12230–12234
93. Van Breusegem F, Bailey-Serres J, Mittler R (2008) Unraveling the tapestry of networks involving reactive oxygen species in plants. Plant Physiol 147:978–984
94. van Dongen JT, Frohlich A, Ramirez-Aguilar SJ, Schauer N, Fernie AR, Erban A, Kopka J, Clark J, Langer A, Geigenberger P (2009) Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of Arabidopsis plants. Ann Bot (Lond) 103:269–280
95. Wang R, Guegler K, LaBrie ST, Crawford NM (2000) Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell Online 12:1491–1509
96. Wulff A, Oliveira HC, Saviani EE, Salgado I (2009) Nitrite reduction and superoxide-dependent nitric oxide degradation by Arabidopsis mitochondria: influence of external NAD(P)H dehydrogenases and alternative oxidase in the control of nitric oxide levels. Nitric Oxide 21:132–139
97. Yan B, Dai Q, Liu X, Huang S, Wang Z (1996) Flooding-induced membrane damage, lipid oxidation and activated oxygen generation in corn leaves. Plant Soil 179:261–268
98. Yoo S, Sheen J (2008) MAPK signaling in plant hormone ethylene signal transduction. Plant Signal Behav 3:848–849
99. Yun B, Feechan A, Yin M, Saidi NBB, Le Bihan T, Yu M, Moore JW, Kang J, Kwon E, Spoel SH, Pallas JA, Loake GJ (2011) S-nitrosylation of NADPH oxidase regulates cell death in plant immunity. Nature 478:264–268
100. Zabalza A, van Dongen JT, Froehlich A, Oliver SN, Faix B, Gupta KJ, Schmalzlin E, Igal M, Orcaray L, Royuela M, Geigenberger P (2009) Regulation of respiration and fermentation to control the plant internal oxygen concentration. Plant Physiol 149:1087–1098
101. Zhao L, Gu R, Gao P, Wang G (2008) A nonsymbiotic hemoglobin gene from maize, ZmHb, is involved in response to submergence, high-salt and osmotic stresses. Plant Cell Tissue Organ Cult 95:227–237
102. Zhao M, Chen L, Zhang L, Zhang W (2009) Nitric reductase-dependent nitric oxide production is involved in cold acclimation and freezing tolerance in Arabidopsis. Plant Physiol 151:755–767