Article | . 2018 Vol. 36, Issue. 2
Correlation Network Analysis of Abiotic Stressrelated Genes Reveals the Coordinated Regulation of Transcription in Chinese Cabbage

Department of Horticultural Biotechnology, Kyung Hee University1
Biosafety Division, National Academy of Agricultural Science, Rural Development Administration2
Division of Crop Science and Biotechnology, Dankook University3

2018.. 266:279


Plant responses to abiotic stresses such as drought, cold, and salt stress include altered expression of genes involved in metabolic processes, including growth, development, and physiological changes. Non-biological stress can lead to changes in the growth and morphology of crops, as well as reduced harvest volume. Plants must respond simultaneously to multiple stresses in the environment; therefore, research on abiotic stress should focus on the interactions of these stress responses. In the present study, we constructed a co-expression network for multidirectional analysis of cold, drought, and salt stress response genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis). We constructed the co-expression network using abiotic stress-related data from the KBGP-24K microarray in the B. rapa Expressed sequence tag data and microarray database (BrEMD) and performed abiotic-stress specific gene expression analyses of B. rapa. The core mechanism underlying abiotic stress tolerance in B. rapa is the inactivation of abscisic acid metabolism, which triggers proline biosynthesis. We also characterized unknown genes possibly related to abiotic stress tolerance by producing transgenic Chinese cabbage lines overexpressing these genes.

1. Angelovici R, Galili G, Fernie AR, Fait A (2010) Seed desiccation: a bridge between maturation and germination. Trends Plant Sci 15:211-2118. doi:10.1016/j.tplants.2010.01.003  

2. Baena-González E, Rolland F, Thevelein JM, Sheen J (2007) A central integrator of transcription networks in plant stress and energy signalling. Nature 448:938-942. doi:10.1038/nature06069  

3. Barnes J, Hut P (1986) A hierarchical O(N log N) force-calculation algorithm. Nature 324:446-449. doi:10.1038/324446a0  

4. Batagelj V, Mrvar A (1998) Pajek-program for large network analysis. Connections 21:47-57  

5. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Statist Soc 57:289-300  

6. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091-1093. doi:10.1093/bioinformatics/btp101  

7. Calzadilla PI, Maiale SJ, Ruiz OA, Escaray FJ (2016) Transcriptome response mediated by cold stress in Lotus japonicus. Front Plant Sci 7:374. doi:10.3389/fpls.2016.00374  

8. Christie PJ, Alfenito MR, Walbot V (1994) Impact of low-temperature stress on general phenylpropanoid and anthocyanin pathways: Enhancement of transcript abundance and anthocyanin pigmentation in maize seedlings. Planta 194:541. doi:10.3389/fpls.2016. 00374  

9. Clauw P, Coppens F, De Beuf K, Dhondt S, Van Daele T, Maleux K, Storme V, Clement L, Gonzalez N, et al. (2015) Leaf responses to mild drought stress in natural variants of Arabidopsis. Plant Physiol 167:800-816. doi:10.1104/pp.114.254284  

10. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-2382. doi:10.1038/nprot.2007.324  

11. Devarenne TP (2011) The plant cell death suppressor Adi3 interacts with the autophagic protein Atg8h. Biochem Biophys Res Commun 412:699-703. doi:10.1016/j.bbrc.2011.08.031  

12. Ehrnsperger M, Gräber S, Gaestel M, Buchner J (1997) Binding of non-native protein to Hsp25 during heat shock creates a reservoir of folding intermediates for reactivation. EMBO J 16:221-229. doi:10.1093/emboj/16.2.221  

13. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178-1186. doi:10.1093/nar/gkr944  

14. Hare P, Cress W (1997) Metabolic implications of stress induced proline accumulation in plants. Plant Growth Regul 21:79-102. doi:10.1023/A:1005703923347  

15. Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ (2000) Plant cellular and molecular responses to high salinity. Annu Rev Plant Mol Plant Physiol 51:463-499. doi:10.1146/annurev.arplant.51.1.463  

16. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57. doi:10.1038/nprot.2008.211  

17. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:D109-114. doi: 10.1093/nar/gkr988  

18. Krasensky J, Jonak C (2012) Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. J Exp Bot 63:1593-1608. doi: 10.1093/jxb/err460  

19. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130:2129-2141. doi: 10.1104/pp.008532  

20. Lechner E, Leonhardt N, Eisler H, Parmentier Y, Alioua M, Jacquet H, Leung J, Genschik P (2011) MATH/BTB CRL3 receptors target the homeodomain-leucine zipper ATHB6 to modulate abscisic acid signaling. Dev Cell 21:1116-1128. doi: 10.1016/j.devcel.2011.10.018  

21. Lee GH, Yu JG, Park JH, Park YD (2014) Construction of a network model to reveal genes related to salt tolerance in Chinese cabbage. Korean J Hortic Sci Technol 32:684-693. doi: 10.7235/hort.2014.14034  

22. Lee GH, Yu JG, Park YD (2015) Time-based expression networks of genes eelated to cold stress in Brassica rapa ssp. pekinensis. Korean J Hortic Sci Technol 33:114-123. doi: 10.7235/hort.2015.14056  

23. Lee GH, Park YD (2017) A Co-expression network of drought stress-related genes in Chinese cabbage. Korean J Hortic Sci Technol 35:243- 251. doi: 10.12972/kjhst.20170027  

24. Lee SC, Lim MH, Kim JA, Lee SI, Kim JS, Jin M, Kwon SJ, Mun JH, Kim YK, et al. (2008) Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24K oligo microarray. Mol Cells 26:595-605. PMID:18797175  

25. Leyva A, Jarillo JA, Salinas J, Martinez-Zapater JM (1995) Low temperature induces the accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs of Arabidopsis thaliana in a light-dependent manner. Plant Physiol 108:39-46. doi:10.1104/ pp.108.1.39  

26. Matysik J, Bhalu B, Mohanty P (2002) Molecular mechanisms of quenching of reactive oxygen species by proline under stress in plants. Curr Sci 82:525-532  

27. Mehterov N, Balazadeh S, Hille J, Toneva V, Mueller-Roeber B, Gechev T (2012) Oxidative stress provokes distinc transcriptional responses in the stress-tolerant atr7 and stress-sensitive loh2 Arabidopsis thaliana mutants as revealed by multiparallel quantitative real-time PCR analysis of ROS marker and antioxidant genes. Plant Physiol Biochem 59:20-29. doi:10.1016/j.plaphy.2012.05.024  

28. Orvar BL, Sangwan V, Omann F, Dhindsa RS (2000) Early steps in cold sensing by plant cells: the role of actin cytoskeleton and membrane fluidity. Plant J 23:785-794. doi:10.1046/j.1365-313x.2000.00845.x  

29. Provart N (2012) Correlation networks visualization. Front Plant Sci 3:240. doi:10.3389/fpls.2012.00240  

30. RDA (the rural development administration) (2008) BrEMD: the Brassica rapa EST and microarray database. http://www.brassica-rapa. org/BrEMD  

31. Ruckle ME, Burgoon LD, Lawrence LA, Sinkler CA, Larkin RM (2012) Plastids are major regulators of light signaling in Arabidopsis. Plant Physiol 159:366-390. doi:10.1104/pp.112.193599  

32. Sangwan V, Foulds I, Singh J, Dhindsa RJ (2001) Cold-activation of Brassica napus BN115 promoter is mediated by structural changes in membranes and cytoskeleton, and requires Ca influx. Plant J 27:1-12. doi:10.1046/j.1365-313x.2001.01052.x  

33. Schulz M, Kussmann P, Knop M, Kriegs B, Gresens F, Eichert T, Ulbrich A, Marx F, Fabricius H, et al. (2007) Allelopathic monoterpenes interfere with Arabidopsis thaliana cuticular waxes and enhance transpiration. Plant Signal Behav 2:231-239. doi:10.4161/ psb.2.4.4469  

34. Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K (2001) Monitoring the expression pattern of 1,300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13: 61-72. doi:10.1105/tpc.13.1.61  

35. Serin EA, Nijveen H, Hilhorst HW, Ligterink W (2016) Learning from co-expression networks: possibilities and challenges. Front Plant Sci 7:444. doi:10.3389/fpls.2016.00444  

36. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504. doi:10.1101/gr.1239303  

37. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 27:431-432. doi:10.1093/bioinformatics/btq675  

38. Strizhov N, Abrahám E, Okrész L, Blickling S, Zilberstein A, Schell J, Koncz C, Szabados L (1997) Differential expression of two P5CS genes controlling proline accumulation during salt-stress requires ABA and is regulated by ABA1, ABI1 and AXR2 in Arabidopsis. Plant J 12:557-569. doi:10.1046/j.1365-313x.1997.00557.x  

39. Szabados L, Savouré A (2010) Proline: a multifunctional amino acid. Trends Plant Sci 15:89-97. doi:10.1016/j.tplants.2009.11.009  

40. Theocharidis A, van Dongen S, Enright AJ, Freeman TC (2009) Network visualization and analysis of gene expression data using BioLayout Express (3D). Nat Protoc 4:1535-1550. doi:10.1038/nprot.2009.177  

41. Tunc-Ozdemir M, Miller G, Song L, Kim J, Sodek A, Koussevitzky S, Misra AN, Mittler R, Shintani D (2009) Thiamin confers enhanced tolerance to oxidative stress in Arabidopsis. Plant Physiol 151:421-432. doi:10.1104/pp.109.140046  

42. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, et al. (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32:1633-1651. doi:10.1111/j.1365-3040. 2009.02040.x  

43. Vierling E (1991) The roles of heat shock proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 42:579-620. doi:10.1146/annurev.pp. 42.060191.003051  

44. Wang W, Vinocur B, Shoseyov O, Altman A (2004) Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 9:244-252. doi:10.1016/j.tplants.2004.03.006  

45. Waters ER, Lee GJ, Vierling E (1996) Evolution, structure and function of the small heat shock proteins in plants. J Exp Bot 47:325-338. doi:10.1093/jxb/47.3.325  

46. Williamson JD, Jennings DB, Guo WW, Pharr DM, Ehrenshaft M (2002) Sugar alcohols, salt stress, fungal resistance: polyols-multifunctional plant protection? J Am Soc Hortic Sci 127:467-473  

47. Xiong L, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14:S165-183. doi:10.1007/s11033- 011-0823-1  

48. Yu JG, Lee GH, Park JH, Park YD (2014a) Characterization and gene co-expression network analysis of a salt tolerance-related gene, BrSSR, in Brassica rapa. Korean J Hortic Sci Technol 32:845-852. doi:10.7235/hort.2014.14040  

49. Yu JG, Lee GH, Lee SC, Park YD (2014b) Gene expression and phenotypic analyses of transgenic Chinese cabbage over-expressing the cold tolerance gene, BrCSR. Hortic Environ Biotechnol 55:415-422. doi:10.1007/s13580-014-0054-1  

50. Yu JG, Lee GH, Park JH, Park YD (2016) Characterization of a drought-tolerance gene, BrDSR, in Chinese cabbage. Korean J Hortic Sci Technol 34:102-111. doi:10.12972/kjhst.20160011  

51. Zang L, Zheng T, Su X (2015) Advances in research of fasciclin-like arabinogalactan proteins (FLAs) in plants. Plant Omics 8:190