Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings

Plant Molecular Biology

Volumn 77, Issue 1, 2011, Pages 129-144

  Nanjo, Yohei ^a   Maruyama, Kyonoshin ^b   Yasue, Hiroshi ^c,d   Yamaguchi Shinozaki, Kazuko ^b,e   Shinozaki, Kazuo ^f   Komatsu, Setsuko ^a  

^a NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

^b JAPAN INTERNATIONAL RESEARCH CENTER FOR AGRICULTURAL SCIENCES   (Japan)

^c NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^d JAPAN AEROSPACE EXPLORATION AGENCY   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

^f RIKEN Center for Sustainable Resource Science   (Japan)

Author keywords

Flooding; Seedling; Soybean; Transcriptome

Indexed keywords

VEGETABLE PROTEIN; WATER;

ARTICLE; DNA MICROARRAY; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PHOTOSYNTHESIS; PHYSIOLOGICAL STRESS; PLANT GROWTH; PLANT ROOT; SEEDLING; SOYBEAN;

ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HYPOCOTYL; METABOLIC NETWORKS AND PATHWAYS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOTOSYNTHESIS; PLANT PROTEINS; PLANT ROOTS; SEEDLING; SOYBEANS; STRESS, PHYSIOLOGICAL; TRANSCRIPTION, GENETIC; WATER;

GLYCINE MAX;

EID: 80051905614     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-011-9799-4     Document Type: Article

References (68)

1. Aoki T, Akashi T, Ayabe S (2000) Flavonoids of leguminous plants, structure, biological activity, and biosynthesis. J Plant Res 113: 475-488.
2. Bailey-Serres J, Voesenek LACJ (2008) Flooding stress, acclimations and genetic diversity. Annu Rev Plant Biol 59: 313-339.
3. 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.
4. Branco-Price C, Kawaguchi R, Ferreira RB, Bailey-Serres J (2005) Genome-wide analysis of transcripts abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot 96: 647-660.
5. 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.
6. Chiba M, Kubo M, Miura T, Sato T, Rezaeian AH, Kiyosawa H, Ohkohchi N, Yasue H (2008) Localization of sense and antisense transcripts of Prdx2 gene in mouse tissues. Cytogenet Genome Res 121: 222-231.
7. Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW (2010) Global gene expression responses to waterlogging in roots and leaves of cotton (gossypium hirsutum L.) Plant Cell Physiol 51: 21-37.
8. Creelman RA, Mullet JE (1995) Jasmonic acid distribution and action in plants: regulation during development and response to biotic and abiotic stress. Proc Natl Acad Sci USA 92: 4114-4119.
9. Creelman RA, Tierney ML, Mullet JE (1992) Jasmonic acid/methyl jasmonate accumulate in wounded soybean hypocotyls and modulate wound gene expression. Proc Natl Acad Sci USA 89: 4938-4941.
10. Devoto A, Piffanelli P, Nilsson I, Wallin E, Panstruga R, von Heijne G, Schulze-Lefert P (1999) Topology, subcellular localization, and sequence diversity of Mlo family in plants. J Biol Chem 274: 34993-35004.
11. Ding L, Pandey S, Assmann SM (2008) Arabidopsis extra-large G proteins (XLGs) regulate root morphogenesis. Plant J 53: 248-263.
12. Drew MC, Cobb BG, Johnson JR, Andrews D, Morgan PW, Jordan W, He CJ (1994) Metabolic acclimation of root tips to oxygen deficiency. Ann Bot 74: 281-286.
13. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-W70.
14. Eulgem T, Somssich IE (2007) Networks of WRKY transcription factors in defense signaling. Curr Opin Plant Biol 10: 366-371.
15. Fennoy SL, Bailey-Serres J (1995) Post-transcriptional regulation of gene expression in oxygen-deprived roots of maize. Plant J 7: 287-295.
16. Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14: 1675-1690.
17. Fukao T, Bailey-Serres J (2004) Plant responses to hypoxia-is survival a balancing act? Trends Plant Sci 9: 449-456.
18. Gibbs J, Greenway H (2003) Mechanisms of anoxia tolerance in plants. I. Growth, survival and anaerobic catabolism. Funct Plant Biol 30: 1-47.
19. Gladish DK, Xu J, Niki T (2006) Apoptosis-like programmed cell death occurs in procambium and ground meristem of pea (Pisum sativum) root tips exposed to sudden flooding. Ann Bot 97: 895-902.
20. Greenberg JT, Ausubel FM (1993) Arabidopsis mutants comprised for the control of cellular damage during pathogenesis and aging. Plant J 4: 327-341.
21. Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH (2007) A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res 17: 632-640.
22. Harada T, Satoh S, Yoshioka T, Ishizawa K (2007) Anoxia-enhanced expression of genes isolated by suppression subtractive hybridization from pondweed (Potamogeton distinctus A. Benn.) turions. Planta 226: 1041-1052.
23. Hashiguchi A, Sakata K, Komatsu S (2009) Proteome analysis of early-stage soybean seedlings under flooding stress. J Proteome Res 8: 2058-2069.
24. Hashimoto Y, Kondo T, Kageyama Y (2008) Lilliputians get into the limelight: novel class of small peptides genes in morphogenesis. Dev Growth Differ 50: S269-S276.
25. Hattori Y, Nagai K, Furukawa S et al (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460: 1026-1031.
26. Huang B, Johnson JW (1995) Root respiration and carbohydrate status of two wheat genotypes in response to hypoxia. Ann Bot 75: 427-432.
27. Jackson MB, Colmer TD (2005) Response and adaptation by plants to flooding stress. Ann Bot 96: 501-505.
28. Jackson MB, Ram PC (2003) Physiological and molecular basis of susceptibility and tolerance of rice plants to complete submergence. Ann Bot 91: 227-241.
29. Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D, Davis RW, Boeke JD, Snyder MA, Basrai MA (2006) Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res 16: 365-373.
30. Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
31. Kirkpatrick MT, Rupe JC, Rothrock CS (2006) Soybean response to flooded soil conditions and the association with soil borne plant pathogenic genera. Plant Dis 90: 592-596.
32. Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES (2002) Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. Plant Cell 14: 2481-2494.
33. Komatsu S, Yamamoto R, Nanjo Y, Mikami Y, Yunokawa H, Sakata K (2009) A comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques. J Proteome Res 8: 4766-4778.
34. Komatsu S, Kobayashi Y, Nishizawa K, Nanjo Y, Furukawa K (2010) Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress. Amino Acids 39: 1435-1449.
35. Kreuzwieser J, Katharine JH, Howell A, Carroll A, Rennenberg H, Millar AH, Whelan J (2009) Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol 149: 461-473.
36. 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.
37. Laskowski M, Biller S, Stanley K, Kajstura T, Prusty R (2006) Expression profiling of auxin-treated Arabidopsis roots: toward a molecular analysis of lateral root emergence. Plant Cell Physiol 47: 788-792.
38. Liu F, Vantoai T, Moy LP, Bock G, Linford LD, Quackenbush J (2005) Global transcription profiling reveals comprehensive insight into hypoxic response in Arabidopsis. Plant Physiol 137: 1115-1129.
39. 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.
40. Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, Wilson LW (2010) Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot 61: 165-177.
41. Mommer L, Visser EJW (2005) Underwater photosynthesis in flooded terrestrial plants: a matter of leaf plasticity. Ann Bot 96: 581-589.
42. Mustroph A, Zanetti ME, Jang CJH, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J (2009) Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia. Proc Natl Acad Sci USA 106: 18843-18848.
43. 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 highlight conserved and plant-specific responses. Plant Physiol 152: 1484-1500.
44. Nanjo Y, Skultety L, Ashraf Y, Komatsu S (2010) Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques. J Proteome Res 9: 3989-4002.
45. Narsai R, Howell KA, Carroll A, Ivanova A, Millar AH, Whelan J (2009) Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings. Plant Physiol 151: 306-322.
46. Neff MM, Chory J (1998) Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during Arabidopsis development. Plant Physiol 118: 27-36.
47. Ogawa T, Pan L, Kawai-Yamada M, Yu LH, Yamamura S, Koyama T, Kitajima S, Ohme-Takagi M, Sato F, Uchimiya H (2005) Functional analysis of Arabidopsis ethylene-responsive element binding protein conferring resistance to Bax and abiotic stress-induced plant cell death. Plant Physiol 138: 1436-1445.
48. Piffanelli P, Zhou F, Casais C, Orme J, Jarosch B, Schaffrath U, Collins NC, Panstruga R, Schulze-Lefert P (2002) The barley mlo modulator of defense and cell death is responsive to biotic and abiotic stress stimuli. Plant Physiol 129: 1076-1085.
49. Pnueli L, Hallak-Herr E, Rozenberg M, Cohen M, Goloubinoff P, Kaplan A, Mittler R (2002) Molecular and biochemical mechanisms associated with dormancy and drought tolerance in the desert legume Retama raetam. Plant J 31: 319-330.
50. Pružinská A, Tanner G, Anders I, Roca M, Hörtensteiner S (2003) Chlorophyll breakdown: pheophorbide a oxygenase is a Rieske-type iron-sulfur protein, encoded by the accelerated cell death 1 gene. Proc Natl Acad Sci USA 100: 15259-15264.
51. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365-386.
52. Russell DA, Wong DML, Sachs MM (1990) The anaerobic responses of soybean. Plant Physiol 92: 401-407.
53. Schmid M, Davison TS, Henz SR, Page UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506.
54. Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 46: 178-183.
55. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31: 279-292.
56. Shi F, Yamamoto R, Shimamura S, Hiraga S, Nakayama N, Nakamura T, Yukawa K, Hachinohe M, Matsumoto H, Komatsu S (2008) Cytosolic ascorbate peroxidase 2 cAPX2. is involved in the soybean response to flooding. Phytochem 69: 1295-1303.
57. Steffens B, Sauter M (2010) G proteins as regulators in ethylene-mediated hypoxia signaling. Plant Signal Behav 5: 375-378.
58. Subbaiah CC, Sachs MM (2003) Molecular and cellular adaptations of maize to flooding stress. Ann Bot 90: 119-127.
59. Tran LSP, Truyen N, Quach TN, Satish K, Guttikonda SK, Aldrich DL, Kumar R, Neelakandan A, Valliyodan B, Nguyen HT (2009) Molecular characterization of stress-inducible GmNAC genes in soybean. Mol Genet Genomics 281: 647-664.
60. Umezawa T, Sakurai T, Totoki Y et al (2008) Sequencing and analysis of approximately 40, 000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res 15: 333-346.
61. Usadel B, Nagel A, Thimm O et al (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol 138: 1195-1204.
62. Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 32: 1211-1229.
63. van Dongen JT, Fröhlich A, Ramírez-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 103: 269-280.
64. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
65. Weisshaar B, Jenkins GI (1998) Phenylpropanoid biosynthesis and its regulation. Curr Opin Plant Biol 1: 251-257.
66. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442: 705-708.
67. Zhang ZX, Zou XL, Tang WH, Zheng YL (2006) Revelation on early response and molecular mechanism of submergence tolerance in maize roots by microarray and suppression subtractive hybridization. Environ Exp Bot 58: 53-63.
68. Zhang Z, Wei L, Zou X, Tao Y, Liu Z, Zheng Y (2008) Submergence-responsive microRNAs are potentially involved in the regulation of morphological and metabolic adaptations in maize root cells. Ann Bot 102: 509-519.