‘Omics’ techniques and their use to identify how soybean responds to flooding

Journal of Analytical Science and Technology

Volumn 6, Issue 1, 2015, Pages

  Komatsu, Setsuko ^a   Sakata, Katsumi ^b   Nanjo, Yohei ^a  

^a NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

^b MAEBASHI INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Flooding; Metabolomics; Omics; Proteomics; Soybean; Transcriptomics

Indexed keywords

EID: 84973534203     PISSN: 20933134     EISSN: 20933371     Source Type: Journal    
DOI: 10.1186/s40543-015-0052-7     Document Type: Review

References (50)

1. Ahsan N, Komatsu S (2009) Comparative analyses of the proteomes of leaves and flowers at various stages of development reveal organ-specific functional differentiation of proteins in soybean. Proteomics 9:4889–4907
2. Bray EA, Bailey-Serres J, Weretilnyk E (2000) Responses to abiotic stresses. In: Buchannan B, Gruissem W, Jones R (eds) Biochemistry and molecular biology of plants. American Society of Plant Biologists, Rockville, MD, USA, pp 1158–1249
3. 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
4. Deshmukh R, Sonah H, Patil G, Chen W, Prince S, Mutava R, Vuong T, Valliyodan B, Nguyen HT (2014) Integrating omic approaches for abiotic stress tolerance in soybean. Front Plant Sci 5:244
5. Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1–15
6. Fiehn O, Kloska S, Altmann T (2001) Integrated studies on plant biology using multiparallel techniques. Curr Opin Biotechnol 12:82–86
7. Fukumura R, Takahashi H, Saito T, Tsutsumi Y, Fujimori A, Sato S, Tatsumi K, Araki R, Abe M (2003) A sensitive transcriptome analysis method that can detect unknown transcripts. Nucleic Acids Res 31:e94
8. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29:644–652
9. Hashiguchi A, Ahsan N, Komatsu S (2010) Proteomics application of crops in the context of climatic changes. Food Res Intl 43:1803–1813
10. Hossain Z, Khatoon A, Komatsu S (2013) Soybean proteomics for unraveling abiotic stress response mechanism. J Proteome Res 12:4670–4684
11. Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30
12. 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
13. Komatsu S (2007) Edman sequencing of proteins from 2D gels. Methods Mol Biol 355:211–217
14. Komatsu S (2009) Western blotting/Edman sequencing using PVDF membrane. Methods Mol Biol 536:163–171
15. Komatsu S, Hossain Z (2013) Organ-specific proteome analysis for identification of abiotic stress response mechanism in crop. Front Plant Sci 4:71
16. Komatsu S, Yanagawa Y (2013) Cell wall proteomics of crops. Front Plant Sci 4:17
17. Komatsu S, Wada T, Abaléa Y, Nouri MZ, Nanjo Y, Nakayama N, Shimamura S, Yamamoto R, Nakamura T, Furukawa K (2009a) Analysis of plasma membrane proteome in soybean and application to flooding stress response. J Proteome Res 8:4487–4499
18. Komatsu S, Yamamoto R, Nanjo Y, Mikami Y, Yunokawa H, Sakata K (2009b) A comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques. J Proteome Res 8:4766–4778
19. 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
20. Komatsu S, Deschamps T, Hiraga S, Kato M, Chiba M, Hashiguchi A, Tougou M, Shimamura S, Yasue H (2011a) Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots. Plant Mol Biol 77:309–322
21. Komatsu S, Yamamoto A, Nakamura T, Nouri MZ, Nanjo Y, Nishizawa K, Furukawa K (2011b) Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques. J Proteome Res 10:3993–4004
22. Komatsu S, Hiraga S, Yanagawa Y (2012a) Proteomics techniques for the development of flood tolerant crops. J Proteome Res 11:68–78
23. Komatsu S, Kuji R, Nanjo Y, Hiraga S, Furukawa K (2012b) Comprehensive analysis of endoplasmic reticulum-enriched fraction in root tips of soybean under flooding stress using proteomics techniques. J Proteomics 77:531–560
24. Komatsu S, Han C, Nanjo Y, Altaf-Un-Nahar M, Wang K, He D, Yang P (2013a) Label-free quantitative proteomic analysis of abscisic acid effect in early-stage soybean under flooding. J Proteome Res 12:4769–4784
25. Komatsu S, Shirasaka N, Sakata K (2013b) ‘Omics’ techniques for identifying flooding-response mechanisms in soybean. J Proteomics 93:169–178
26. Komatsu S, Hiraga S, Nouri MZ (2014a) Analysis of flooding-responsive proteins localized in the nucleus of soybean root tips. Mol Biol Rep 41:1127–1139
27. Komatsu S, Nakamura T, Sugimoto Y, Sakamoto K (2014b) Proteomic and metabolomic analyses of soybean root tips under flooding stress. Protein Pept Lett 21:865–884
28. Komatsu S, Oh MW, Jang HY, Kwon SJ, Kim HR, Ko JH, Woo SH, Nanjo Y (2014c) Proteomic analyses of soybean root tips during germination. Protein Pept Lett 21:1308–1319
29. 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
30. Mittler R, Blumwald E (2010) Genetic engineering for modern agriculture: challenges and perspectives. Annu Rev Plant Biol 61:443–462
31. Mustafa G, Komatsu S (2014) Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress. Front Plant Sci 5:627
32. Nakamura T, Yamamoto R, Hiraga S, Nakayama N, Okazaki K, Takahashi H, Uchimiya H, Komatsu S (2012) Evaluation of metabolite alteration under flooding stress in soybeans. Jpn Agric Res Q 46:237–248
33. 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
34. Nanjo Y, Maruyama K, Yasue H, Yamaguchi-Shinozaki K, Shinozaki K, Komatsu S (2011a) Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings. Plant Mol Biol 77:129–144
35. Nanjo Y, Nouri MZ, Komatsu S (2011b) Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary. Phytochemistry 2:1263–1272
36. Nanjo Y, Skultety L, Uváčková L, Klubicová K, Hajduch M, Komatsu S (2012) Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings. J Proteome Res 11:372–385
37. Oh MW, Nanjo Y, Komatsu S (2014) Identification of nuclear proteins in soybean under flooding stress using proteomic technique. Protein Pept Lett 21:458–467
38. Ohyanagi H, Sakata K, Komatsu S (2012) Soybean Proteome Database 2012: update on the comprehensive data repository for soybean proteomics. Front Plant Sci 3:110
39. Putri SP, Yamamoto S, Tsugawa H, Fukusaki E (2013) Current metabolomics: technological advances. J Biosci Bioeng 116:9–16
40. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I (2010) De novo assembly and analysis of RNA-seq data. Nat Meth 7:909–912
41. Sakata K, Ohyanagi H, Nobori H, Nakamura T, Hashiguchi A, Nanjo Y, Mikami Y, Yunokawa H, Komatsu S (2009) Soybean proteome database: a data resource for plant differential omics. J Proteome Res 8:3539–3548
42. Sultan M, Schulz MH, Richard H (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956–960
43. Takahashi H, Hotta Y, Hayashi M, Kawai-Yamada M, Komatsu S, Uchimiya H (2005) High throughput metabolome and proteome analysis of transgenic rice plants (Oryza sativa L.). Plant Biotech 22:47–50
44. Tamang BG, Magliozzi JO, Maroof MAS, Fukao T (2014) Physiological and transcriptomic characterization of submergence and reoxygenation responses in soybean seedlings. Plant Cell Environ 37:2350–2365
45. Tougou M, Hashiguchi A, Yukawa K, Nanjo Y, Hiraga S, Nakamura T, Nishizawa K, Komatsu S (2012) Responses to flooding stress in soybean seedlings with the alcohol dehydrogenase transgene. Plant Biotechnol 29:301–305
46. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Gen 10:57–63
47. Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803
48. Yanagawa Y, Komatsu S (2012) Ubiquitin/proteasome-mediated proteolysis is involved in the response to flooding stress in soybean roots, independent of oxygen limitation. Plant Sci 185–186:250–258
49. Yin X, Sakata K, Komatsu S (2014) Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress. J Proteome Res 13:5618–5634
50. Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 12:1–12