Vinogradov SN, Hoogewijs D, Bailly X, Arrendondo-Peter R, Gough J, Dewilde S, Moens L, Vanfleteren JR: A phylogenomic profile of globins. BMC Evolutionary Biology. 2006, 6: 31-10.1186/1471-2148-6-31.
Article
PubMed
PubMed Central
Google Scholar
Hoy JA, Hargrove MS: The structure and function of plant hemoglobins. Plant Physiol Biochem. 2008, 46: 371-379. 10.1016/j.plaphy.2007.12.016.
Article
PubMed
CAS
Google Scholar
Jokipii-Lukkari S, Frey AD, Kallio PT, Häggman H: Intrinsic non-symbiotic and truncated haemoglobins and heterologous Vitreoscilla haemoglobin expression in plants. J Exp Bot. 2009, 60: 409-422. 10.1093/jxb/ern320.
Article
PubMed
CAS
Google Scholar
Dordas C, Rivoal J, Hill RD: Plant haemoglobins, nitric oxide and hypoxic stress. Ann Bot. 2003, 91: 173-178. 10.1093/aob/mcf115.
Article
PubMed
CAS
PubMed Central
Google Scholar
Borisjuk L, Macherel D, Benamar A, Wobus U, Rolletschek H: Low oxygen sensing and balancing in plant seeds - a role for nitric oxide. New Phytologist. 2007, 176: 813-823. 10.1111/j.1469-8137.2007.02226.x.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sowa AW, Duff SMG, Guy PA, Hill RD: Altering hemoglobin levels changes energy status in maize cells under hypoxia. PNAS. 1998, 95: 10317-10321. 10.1073/pnas.95.17.10317.
Article
PubMed
CAS
PubMed Central
Google Scholar
Dordas C, Hasinoff BB, Igamberdiev AU, Manac'h N, Rivoal J, Hill RD: Expression of a stress-induced hemoglobin affects NO levels produced by alfalfa root cultures under hypoxic stress. Plant J. 2003, 35: 763-770. 10.1046/j.1365-313X.2003.01846.x.
Article
PubMed
CAS
Google Scholar
Perazzolli M, Dominici P, Romero-Puertas MC, Zago E, Zeier J, Sonoda M, Lamb C, Delledonne M: Arabidopsis nonsymbiotic hemoglobin Ahb1 modulates nitric oxide bioactivity. Plant Cell. 2004, 16: 2785-2794. 10.1105/tpc.104.025379.
Article
PubMed
CAS
PubMed Central
Google Scholar
Neill SJ, Desikan R, Hancock JT: Nitric oxide signaling in plants. New Phytologist. 2003, 159: 11-35. 10.1046/j.1469-8137.2003.00804.x.
Article
CAS
Google Scholar
Benamar A, Rolletschek H, Borisjuk L, Avelange-Macherel MH, Curien G, Mostefai A, Andriantsitohaina R, Macherel D: Nitrite-nitric oxide control of mitochondrial respiration at the frontier of anoxia. Biochim Biophys Acta. 2008, 1777: 1268-1275. 10.1016/j.bbabio.2008.06.002.
Article
PubMed
CAS
Google Scholar
Gas E, Flores-Perez U, Sauret-Güeto S, Rodriguez-Concepcion M: Hunting for plant nitric oxide synthase provides new evidence of a central role for plastids in nitric oxide metabolism. Plant Cell. 2009, 21: 18-23. 10.1105/tpc.108.065243.
Article
PubMed
CAS
PubMed Central
Google Scholar
Borisjuk L, Rolletschek H: The oxygen status in the developing seeds. New Phytologist. 2009, 182: 17-30. 10.1111/j.1469-8137.2008.02752.x.
Article
PubMed
CAS
Google Scholar
Geigenberger P: Response of plant metabolism to too little oxygen. Curr Opin Plant Biol. 2003, 6: 247-56. 10.1016/S1369-5266(03)00038-4.
Article
PubMed
CAS
Google Scholar
Gibon Y, Vigeolas H, Tiessen A, Geigenberger P, Stitt M: Sensitive and high throughput metabolite assays for inorganic pyrophosphate, ADPGlc, nucleotide phosphates, and glycolytic intermediates based on a novel enzymic cycling system. Plant J. 2002, 30: 221-235. 10.1046/j.1365-313X.2001.01278.x.
Article
PubMed
CAS
Google Scholar
Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES: Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. Plant Cell. 2002, 14: 2481-2494. 10.1105/tpc.004747.
Article
PubMed
CAS
PubMed Central
Google Scholar
Liu F, Toai TV, Moy LP, Bock G, Linford LD, Quackkenbush J: Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiol. 2005, 137: 1115-1129. 10.1104/pp.104.055475.
Article
PubMed
CAS
PubMed Central
Google Scholar
Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J: Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J. 2008, 56: 743-755. 10.1111/j.1365-313X.2008.03642.x.
Article
PubMed
CAS
Google Scholar
Mustroph A, Zanetti ME, Jang CJH, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J: Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. PNAS. 2009, 106: 18843-18848. 10.1073/pnas.0906131106.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bäumlein H, Boerjan W, Nagy I, Panitz R, Inze D, Wobus U: Upstream sequences regulating legumin gene expression in heterologous transgenic plants. Mol Gen Genet. 1991, 225: 121-128.
PubMed
Google Scholar
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M: MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004, 37: 914-939. 10.1111/j.1365-313X.2004.02016.x.
Article
PubMed
CAS
Google Scholar
Wagner TA, Kohorn BD: Wall-associated kinases are expressed throughout plant development and are required for cell expansion. Plant Cell. 2001, 13: 303-318. 10.1105/tpc.13.2.303.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kohorn BD, Kobayashi M, Johanson S, Friedman HP, Fischer A, Byers N: Wall-assocoated kinase 1 (WAK1) is crosslinked in endomembranes, and transport to the cell surface requires correct cell-wall synthesis. J Cell Sci. 2006, 119: 2282-2290. 10.1242/jcs.02968.
Article
PubMed
CAS
Google Scholar
Blanco F, Garreton V, Frey N, Dominguez C, Perez-Acle T, Van der Straeten D, Jordana X, Holuigue L: Identification of NPR1-dependent and independent genes early induced by salicylic acid treatment in Arabidopsis. Plant Mol Biol. 2005, 59: 927-944. 10.1007/s11103-005-2227-x.
Article
PubMed
CAS
Google Scholar
Pitorre D, Llauro C, Jobet E, Guilleminot J, Brizard JP, Delseny M, Lasserre E: RLK7, a leucine-rich repeat receptor-like kinase, is required for proper germination speed and tolerance to oxidative stress in Arabidopsis thaliana. Planta. 2010, 232: 1339-53. 10.1007/s00425-010-1260-4.
Article
PubMed
CAS
Google Scholar
Stone SL, Callis J: Ubiquitin ligases mediate growth and development by promoting protein death. Curr Opin Plant Biol. 2007, 10: 624-632. 10.1016/j.pbi.2007.07.010.
Article
PubMed
CAS
Google Scholar
Gomez LD, Baud S, Gilday A, Li Y, Graham IA: Delayed embryo development in the ARABIDOPSIS TREHALOSE-6-PHOSPHATE SYNTHASE 1 mutant is associated with altered cell wall structure, decreased cell division and starch accumulation. Plant J. 2006, 46: 69-84. 10.1111/j.1365-313X.2006.02662.x.
Article
PubMed
CAS
Google Scholar
Otegui MS, Noh YS, Martinez DE, Petroff MGV, Staehelin LA, Amasino RM, Guiamet JJ: Senescence-associated vacuoles with intense proteolytic activity develop in leaves of Arabidopsis and soybean. Plant J. 2005, 41: 831-844. 10.1111/j.1365-313X.2005.02346.x.
Article
PubMed
CAS
Google Scholar
Hunter PR, Craddock CP, Di Benedetto S, Roberts LM, Frigerio L: Fluorescent reporter proteins for the tonoplast and the vacuolar lumen identify a single vacuolar compartment in Arabidopsis cells. Plant Physiol. 2007, 145: 1371-1382. 10.1104/pp.107.103945.
Article
PubMed
CAS
PubMed Central
Google Scholar
Meyer PE, Lafitte F, Bontempi G: Minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics. 2008, 9: 461-10.1186/1471-2105-9-461.
Article
PubMed
PubMed Central
Google Scholar
McCabe PF, Valentine TA, Forsberg LS, Pennell RI: Soluble signals from cells identified at the cell wall establish a developmental pathway in carrot. Plant Cell. 1997, 9: 2225-2241. 10.1105/tpc.9.12.2225.
Article
PubMed
CAS
PubMed Central
Google Scholar
Seifert GJ, Roberts K: The biology of arabinogalactan proteins. Ann Rev Plant Biol. 2007, 58: 137-161. 10.1146/annurev.arplant.58.032806.103801.
Article
CAS
Google Scholar
Greer S, Wen M, Bird D, Wu X, Samuels L, Kunst L, Jetter R: The cytochrome P450 enzyme CYP96A15 is the midchain alkane hydroxylase responsible for formation of secondary alcohols and ketones in stem cuticular wax of Arabidopsis. Plant Physiol. 2007, 145: 653-667. 10.1104/pp.107.107300.
Article
PubMed
CAS
PubMed Central
Google Scholar
Fowler TJ, Bernhardt C, Tierney ML: Characterization and expression of four proline-rich cell wall protein genes in Arabidopsis encoding two distinct subsets of multiple domain proteins. Plant Physiol. 1999, 121: 1081-1091. 10.1104/pp.121.4.1081.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kim DJ, Smith SM: Molecular cloning of cucumber phosphoenolpyruvate carboxykinase and developmental regulation of gene expression. Plant Mol Biol. 1994, 26: 423-434. 10.1007/BF00039551.
Article
PubMed
CAS
Google Scholar
Manac'h-Little N, Igamberdiev AU, Hill RD: Hemoglobin expression affects ethylene production in maize cell cultures. Plant Physiol Biochem. 2005, 43: 485-489.
Article
PubMed
Google Scholar
Bailey-Serres J, Chang R: Sensing and signaling in response to oxygen deprivation in plants and other organisms. Ann Bot. 2005, 96: 507-518. 10.1093/aob/mci206.
Article
PubMed
CAS
PubMed Central
Google Scholar
Davletova S, Schlauch K, Coutu J, Mittler R: The zinc finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Phys. 2005, 139: 847-856. 10.1104/pp.105.068254.
Article
CAS
Google Scholar
Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, Bailey-Serres J: Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiol. 2010, 152: 1484-1500. 10.1104/pp.109.151845.
Article
PubMed
CAS
PubMed Central
Google Scholar
Paul MJ, Primavesi LF, Jhurreea D, Zhang Y: Trehalose metabolism and signaling. Annu Rev Plant Biol. 2008, 59: 417-441. 10.1146/annurev.arplant.59.032607.092945.
Article
PubMed
CAS
Google Scholar
Igamberdiev AU, Stoimenova M, Seregelyes C, Hill RD: Class-1 hemoglobin and antioxidant metabolism in alfalfa roots. Planta. 2006, 223: 1041-1046. 10.1007/s00425-005-0145-4.
Article
PubMed
CAS
Google Scholar
Xi DM, Liu WS, Yang GD, Wu CA, Zheng CC: Seed-specific overexpression of antioxidant genes in Arabidopsis enhances oxidative stress tolerance during germination and early seedling growth. Plant Biotechnology J. 2010, 8: 796-806. 10.1111/j.1467-7652.2010.00509.x.
Article
CAS
Google Scholar
Dean JV, Harper JE: Nitric oxide and nitrous oxide production by soybean and winged bean during the in vivo nitrate reductase assay. Plant Physiol. 1986, 82: 718-723. 10.1104/pp.82.3.718.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rockel P, Strube F, Rockel A, Wildt J, Kaiser WM: Regulation of nitric oxide (NO) production by plant nitrate reductase in vivo and in vitro. J Exp Bot. 2002, 53: 103-110. 10.1093/jexbot/53.366.103.
Article
PubMed
CAS
Google Scholar
Yamasaki H, Sakihama Y: Simultaneous production of nitrite oxide and peroxynitrite by plant nitrate reductase: In vitro evidence for the NR-dependent formation of active nitrogen species. FEBS Lett. 2000, 468: 89-92. 10.1016/S0014-5793(00)01203-5.
Article
PubMed
CAS
Google Scholar
Kaiser WM, Weiner H, Kandlbinder A, Tsai CB, Rockel P, Sonoda M, Planchet E: Modulation of nitrate reductase: some new insights, an unusual case and a potentially important side reaction. J Exp Bot. 2002, 53: 875-882. 10.1093/jexbot/53.370.875.
Article
PubMed
CAS
Google Scholar
Morot-Gaudry-Talarmain Y, Rockel P, Moreaux T, Quillere I, Leydecker MT, Kaiser WM, Morot-Gaudry JF: Nitrite accumulation and nitritc oxide emission in relation to cellular signaling in nitrite reductase antisense tobacco. Planta. 2002, 215: 708-715. 10.1007/s00425-002-0816-3.
Article
PubMed
CAS
Google Scholar
Desikan R, Griffiths R, Hancock J, Neill S: A new role for an old enzyme: nitrate reductase-mediated nitric oxide generation is required for abscisic acid-induced stomatal closure in Arabidopsis thaliana. PNAS. 2002, 99: 16314-16318. 10.1073/pnas.252461999.
Article
PubMed
CAS
PubMed Central
Google Scholar
Fabre N, Reiter IM, Becuwe-Linka N, Genty B, Rumeau D: Characterization and expresssion analysis of genes encoding alpha and beta carbonic anhydrases in Arabidopsis. Plant Cell Environ. 2007, 30: 617-629. 10.1111/j.1365-3040.2007.01651.x.
Article
PubMed
CAS
Google Scholar
Martin V, Villareal F, Miras I, Navaza A, Haouz A, Gonzales-Lebrero RM, Kaufman SB, Zabaleta E: Recombinant plant gamma carbonic anhydrase homotrimers bind inorganic carbon. FEBS Lett. 2009, 583: 3425-3430. 10.1016/j.febslet.2009.09.055.
Article
PubMed
CAS
Google Scholar
Dordas C, Hasinoff BB, Rivoal J, Hill RD: Class 1 hemoglobins, nitrate and NO levels in hypoxic maize cell suspension cultures. Planta. 2004, 219: 66-72. 10.1007/s00425-004-1212-y.
Article
PubMed
CAS
Google Scholar
Wang P, Du Y, Li Y, Ren D, Song CP: Hydrogen peroxide-mediated activation of MAP Kinase 6 modulates nitric oxide biosynthesis and signal transduction in Arabidopsis. Plant Cell. 2010, 22: 2981-2998. 10.1105/tpc.109.072959.
Article
PubMed
CAS
PubMed Central
Google Scholar
Durner J, Wendehenne D, Klessig DF: Defence gene induction in tobacco by nitric oxide, cyclic GMP, and cyclic ADP-ribose. PNAS. 1998, 95: 10328-10333. 10.1073/pnas.95.17.10328.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ma W, Smigel A, Tsai YC, Braam J, Berkowitz GA: Innate immunity signaling: cytosolic Ca2+ elevation is linked to downstream nitric oxide generation through the action of calmodulin or a calmodulin-like protein. Plant Physiol. 2008, 148: 818-828. 10.1104/pp.108.125104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nie X, Durnin DC, Igamberdiev AU, Hill RD: Cytosolic calcium is involved in the regulation of barley haemoglobin gene expression. Planta. 2006, 223: 542-549. 10.1007/s00425-005-0094-y.
Article
PubMed
CAS
Google Scholar
Lamotte O, Courtois C, Dobrowolska G, Besson A, Pugin A, Wendehenne D: Mechanisms of nitric-oxide-induced increase of free cytosolic Ca2+ concentration in Nicotiana plumbaginifolia cells. Free Radic Biol Med. 2006, 40: 1369-1376. 10.1016/j.freeradbiomed.2005.12.006.
Article
PubMed
CAS
Google Scholar
Besson-Bard A, Courtois C, Gauthier A, Dahan J, Dobrowolska G, Jeandroz S, Pugin A, Wendehenne D: Nitric oxide in plants: production and cross-talk with Ca2+ signaling. Mol Plant. 2008, 1: 218-228. 10.1093/mp/ssm016.
Article
PubMed
CAS
Google Scholar
Bethke PC, Libourel IG, Aoyama N, Chung YY, Stil, DW, Jones RL: The Arabidopsis aleurone layer responds to nitric oxide, gibberellin, and abscisic acid and is sufficient and necessary for seed dormancy. Plant Physiol. 2007, 143: 1173-1188. 10.1104/pp.106.093435.
Article
PubMed
CAS
PubMed Central
Google Scholar
Parani M, Rudrabhatla S, Myers R, Weirich H, Smith B, Leaman DW, Goldman SL: Microarray analysis of nitric oxide responsive transcripts in Arabidopsis. Plant Biotechnology J. 2004, 2: 359-366. 10.1111/j.1467-7652.2004.00085.x.
Article
CAS
Google Scholar
Palmieri MC, Sell S, Huang X, Scherf M, Werner T, Durner J, Lindermayr C: Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach. J Exp Bot. 2008, 59: 177-186. 10.1093/jxb/erm345.
Article
PubMed
CAS
Google Scholar
Yamasaki H, Shimoji H, Ohshiro Y, Sakihama Y: Inhibitory effects of nitric oxide on oxidative phosphorylation in plant mitochondria. Nitric Oxide: Biology and Chemistry. 2001, 5: 261-270. 10.1006/niox.2001.0353.
Article
CAS
Google Scholar
Zottini M, Formentin E, Scattolin M, Carimi F, Schiavo FL, Terzi M: Nitric oxide affects plant mitochondrial functionality in vivo. FEBS Lett. 2002, 515: 75-78. 10.1016/S0014-5793(02)02438-9.
Article
PubMed
CAS
Google Scholar
Clough SJ, Ben AF: Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998, 16: 735-743. 10.1046/j.1365-313x.1998.00343.x.
Article
PubMed
CAS
Google Scholar
Murashige T, Skoog F: A revised medium for rapid growth and bio-assays with tobacco tissue cultures. Physiol Plant. 1962, 15: 473-497. 10.1111/j.1399-3054.1962.tb08052.x.
Article
CAS
Google Scholar
Heim U, Weber H, Bäumlein H, Wobus U: A sucrose-synthase gene of Vicia faba: Expression pattern in developing seeds in relation to starch synthesis and metabolic regulation. Planta. 1993, 191: 394-401. 10.1007/BF00195698.
Article
PubMed
CAS
Google Scholar
Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics. 2003, 19: 185-193. 10.1093/bioinformatics/19.2.185.
Article
PubMed
CAS
Google Scholar
Smyth GK: Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor. Edited by: R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber. Springer, New York; 2005,397-420. full_text.
Chapter
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach for multiple testing. J R Statist Soc B. 1995, 57: 289-300.
Google Scholar
Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JC, Collery M, Girke T: Annotating genes of known and unknown function by large- scale coexpression analysis. Plant Physiol. 2008, 147: 41-57. 10.1104/pp.108.117366.
Article
PubMed
CAS
PubMed Central
Google Scholar
Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods. 2001, 25: 402-408. 10.1006/meth.2001.1262.
Article
PubMed
CAS
Google Scholar
Planchet E, Kaiser WM: Nitric oxide (NO) detection by DAF fluorescence and chemiluminescence: a comparison using abiotic and biotic NO sources. J Exp Bot. 2006, 57: 3043-3055. 10.1093/jxb/erl070.
Article
PubMed
CAS
Google Scholar
Lunn JE, Feil R, Hendriks JHM, Gibon Y, Morcuende R, Osuna D, Scheible WR, Carillo P, Hajirezaei MR, Stitt M: Sugar-induced increases in trehalose 6-phosphate are correlated with redox activation of ADPglucose pyrophosphorylase and higher rates of starch synthesis in Arabidopsis thaliana. Biochem J. 2006, 397: 139-148. 10.1042/BJ20060083.
Article
PubMed
CAS
PubMed Central
Google Scholar
Thiel J, Müller M, Weschke W, Weber H: Amino acid metabolism at the maternal-filial boundary of young barley seeds: a microdissection-based study. Planta. 2009, 230: 205-213. 10.1007/s00425-009-0935-1.
Article
PubMed
CAS
Google Scholar
Rolletschek H, Koch K, Wobus U, Borisjuk L: Positional cues for the starch/lipid balance in maize kernels and resource partitioning to the embryo. Plant J. 2005, 42: 69-83. 10.1111/j.1365-313X.2005.02352.x.
Article
PubMed
CAS
Google Scholar
Borisjuk L, Nguyen TH, Neuberger T, Rutten T, Tschiersch H, Claus B, Feussner I, Webb AG, Jacob P, Webe H, Wobus U, Rolletschek H: Gradients of lipid storage, photosynthesis and plastid differentiation in developing soybean seeds. New Phytologist. 2005, 167: 761-776. 10.1111/j.1469-8137.2005.01474.x.
Article
PubMed
CAS
Google Scholar
Junker BH, Klukas C, Schreiber F: VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006, 7: 109-10.1186/1471-2105-7-109.
Article
PubMed
PubMed Central
Google Scholar