Cdna-aflp analysis reveals differential gene expression in response to salt stress in brachypodium distachyon

Genes and Genomics

Volumn 34, Issue 5, 2012, Pages 475-484

  Kim, Dae Yeon ^a   Hong, Min Jeong ^a   Jang, Ji Hee ^a   Seo, Yong Weon ^a  

^a Korea University   (South Korea)

Author keywords

Brachypodium distachyon; CDNA AFLP; Salt stress; Semi quantitative RT PCR

Indexed keywords

2 OXOGLUTARIC ACID; ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATASE (CALCIUM); CALCIUM BINDING PROTEIN; CASEIN KINASE I LIKE PROTEIN; CASEIN KINASE IDELTA; COMPLEMENTARY DNA; ENZYME; HYDROLASE; PLANT PROTEIN; PROTEIN KINASE; PROTEIN PHOSPHATASE 2C; PROTEIN SERINE THREONINE KINASE; TRANSFERASE; UNCLASSIFIED DRUG;

ABIOTIC STRESS; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BRACHYPODIUM; DNA SEQUENCE; ENZYME ACTIVITY; GENE EXPRESSION; NONHUMAN; PLANT DEVELOPMENT; PLANT GENE; PLANT GROWTH; PROTEIN BINDING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SALT STRESS;

EID: 84865562846     PISSN: 19769571     EISSN: 20929293     Source Type: Journal    
DOI: 10.1007/s13258-012-0067-z     Document Type: Article

References (67)

1. Abramoff MD, Magelhaes PJ, and Ram SJ (2004) Image processing with ImageJ. Biophotonic. Internat. 11: 36-42.
2. Albrecht V, Weinl S, Blazevic D, D’Angelo C, Batistic O, Kolukisaoglu U, Bock R, Schulz B, Harter K, and Kudla J (2003) The calcium sensor CBL1 integrates plant responses to abiotic stresses. Plant J. 36: 457-470.
3. Anzelotti D and Ibrahim R (2000) Novel flavonol 2-oxoglutar-atedependent dioxygenase: affinity purification, characterization and kinetic properties. Archiv. Biochem. Biophys. 382:161-172.
4. Baisakh N, Subudhi PK, and Parami NP (2006) cDNA-AFLP analysis reveals differential gene expression in response to salt stress in a halophyte Spartina alterniflora Loisel. Plant Sci. 170: 1141-1149.
5. +-ATPase and upregulat-ing its transport activity. Mol. Cell Biol. 27: 7781-7790.
6. Beßer K, Jarosch B, Langen G, and Kogel KH (2001) Expression analysis of genes induced in barley after chemical activation reveals distinct disease resistance pathways. Mol. Plant Pathol. 1: 277-286.
7. Chae L, Sudat S, Dudoit S, Zhu T, and Luan S (2009) Diverse transcriptional programs associated with environmental stress and hormones in the Arabidopsis receptor-like kinase gene family. Mol. Plant 2: 84-107.
8. Capoen W, Den Herder J, Sun J, Verplancke C, De Keyser A, De Rycke R, Goormachtig S, Oldroyd G, and Holsters M (2009) Calcium spiking patterns and the role of the calcium/calm-odulin-dependent kinase CCaMK in lateral root base nodulation of Sesbania rostrata. Plant Cell 21: 1526-1540.
9. 2+ antiporter CAX1 to integrate calcium transport and salt tolerance. J. Biol. Chem. 279: 2922-2926.
10. Cheng Y, Zhou W, El sheery NI, Peters C, Li M, Wang X, and Huang J (2011) Characterization of the Arabidopsis glyceropho-sphodiester phosphodiesterase (GDPD) family reveals a role of the plastid-localized AtGDPD1 in maintaining cellular phosphate homeostasis under phosphate starvation. Plant J. 66: 781-795
11. Claverie M, Souquet M, Jean J, Forestier-Chiron N, Lepitre V, Pré M, Jacobs J, Llewellyn D, and Lacape JM (2011) DNA-A-FLP-based genetical genomics in cotton fibers. Theor Appl Genet. doi: 10.1007/s00122-011-1738-x.
12. Dievart A and Clark SE (2003) Using mutant alleles to determine the structure and function of leucine-rich repeat receptor-like kinases. Curr. Opin. Plant Biol. 6: 507-516.
13. Ding YH, Liu NY, Tang ZS, Liu J, and Yang WC (2006) Arabidopsis GLUTAMINE-RICH PROTEIN23 is essential for early embryogenesis and encodes a novel nuclear PPR motif protein that interacts with RNA polymerase II subunit III. Plant Cell 18: 815-830.
14. Donson J, Fang Y, Espiritu-Santo G, Xing W, Salazar A, Miyamoto S, Armendarez V, and Volkmuth W (2002) Comprehensive gene expression analysis by transcript profiling. Plant Mol. Biol. 48: 75-97.
15. Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, and Routledge APM (2001) Brachypodium distachyon: a new model system for functional genomics in grasses. Plant Physiol. 127: 1539-1555.
16. Feng H, Wang X, Sun Y, Wang X, Chen X, Guo J, Duan Y, Huang L, and Kang Z (2011) Cloning and characterization of a calcium binding EF-hand protein gene TaCab1 from wheat and its expression in response to Puccinia striiformis f. sp. tritici and abiotic stresses. Mol. Biol. Rep. 38: 3857-3866.
17. 2+-binding helix-loop-helix EF-hand motifs. Biochem. J. 405: 199-221.
18. Gomès E, Jakobsen MK, Axelsen KB, Geisler M, and Palmgren MG (2000) Chilling tolerance in Arabidopsis involves ALA1, a member of a new family of putative aminophospholipid translocases. Plant Cell 12: 2441-2453.
19. Hase Y, Yokoyama S, Muto A and Himeno H (2009) Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells. RNA 15:1766-1774.
20. Hong Y, Zhang W, Wang X (2010) Phospholipase D and phosphatidic acid signalling in plant response to drought and salinity. Plant Cell Environ. 33: 627-35.
21. Hong Y, Zhang W, and Wang X (2010) Phospholipase D and phosphatidic acid signalling in plant response to drought and salinity. Plant Cell Environ. 33: 627-35.
22. Hua X, Songa F, and Zheng Z (2006) Molecular characterization and expression analysis of a rice protein phosphatase 2C gene, OsBIPP2C1, and overexpression in transgenic tobacco conferred enhanced disease resistance and abiotic tolerance. Physiol. Plant 127: 225-236.
23. Kaothien P, Ok SH, Shuai B, Wengier D, Cotter R, Kelley D, Kiriakopolos S, Muschietti J, and McCormick S, (2005) Kinase partner protein interacts with the LePRK1 and LePRK2 receptor kinases and plays a role in polarized pollen tube growth. Plant J. 42: 492-503.
24. Kim HU and Huang AH (2004) Plastid lysophosphatidyl acyltransferase is essential for embryo development in Arabidopsis. Plant Physiol. 134: 1206-1216.
25. Kim HU, Li Y, and Huang AH (2005) Ubiquitous and endoplasmic reticulum-located lysophosphatidyl acyltransferase, LPAT2, is essential for female but not male gametophyte development in Arabidopsis. Plant Cell 17: 1073-1089.
26. Kim SY, Sivaguru M, and Stacey G (2006) Extracellular ATP in plants. Visualization, localization, and analysis of physiological significance in growth and signaling. Plant Physiol. 142:984-992.
27. Knight H, Trewavas AJ, and Knight MR (1997) Calcium signalling in Arabidopsis thaliana responding to drought and salinity. Plant J. 12: 1067-1078.
28. Kobayashi K, Suzuki M, Tang J, Nagata N, Seki H, Ohyama K, Kiuchi R, Kaneko Y, Matsumoto S, Yoshida S, and Muranaka T (2007) Lovastatin insensitive 1, encoding a novel pentatricopeptide repeat protein, is a potential regulatory factor of isoprenoid biosynthesis in Arabidopsis. Plant Cell Physiol. 48: 322-332.
29. Koussevitzky S, Nott A, Mockler TC, Hong F, Sachetto-Martins G, Surpin M, Lim J, Mittler R, and Chory J (2007) Signals from chloroplasts converge to regulate nuclear gene expression. Science 316: 715-719.
30. Laluk K, AbuQamar S, and Mengiste T (2011) The Arabidopsis mi-tochondria-localized pentatricopeptide repeat protein PGN functions in defense against necrotrophic fungi and abiotic stress tolerance. Plant Physiol. 156: 2053-2068.
31. Lanteri ML, Pagnussat GC, and Lamattina L (2006) Calcium and cal-cium-dependent protein kinases are involved in nitric oxide- and auxin-induced adventitious root formation in cucumber. J. Exp. Bot. 57: 1341-1351.
32. Läuchli A and Lüttge U (2002) Salinity: Environment-plants-mo-lecules. Kluwer Academic Publishers, Dordrecht, the Netherlands, pp ix-x.
33. Lee SC, Choi DS, Hwang IS, and Hwang BK (2010) The pepper oxidoreductase CaOXR1 interacts with the transcription factor CaRAV1 and is required for salt and osmotic stress tolerance. Plant Mol. Bio. 173: 409-424.
34. Liang HE, Fu-Hua LI, Li-Na SHA, Feng-Ling FU, and Wan-Chen LI (2008) Activity of serine/threonine Protein Phosphatase Type-2C (PP2C) and its relationships to drought tolerance in maize. Acta Agron. Sin. 34: 899-903.
35. Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, et al. (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16: 2089-2103.
36. Mahajan S, Pandey GK, and Tuteja N (2008) Calcium- and salt-stress signaling in plants: shedding light on SOS pathway. Arch. Biochem. Biophys. 471: 146-158.
37. Mian AA, Senadheera P, and Maathuis FJM (2009) Improving crop salt tolerance: anion and cation transporters as genetic engineering targets. Plant Stress 5: 64-72.
38. Mignot E and Takahashi JS (2007) A circadian sleep disorder reveals a complex clock. Cell 128: 22-23.
39. Morillo SA and Tax FE (2006) Functional analysis of receptor-like kinases in monocots and dicots. Curr. Opin. in Plant Biol. 9: 460-469
40. Munns R and Tester M (2008) Mechanisms of salinity tolerance. Annu. Rev. Plant Biol. 59: 651-681.
41. Nickson TE (2008) Planning environmental risk assessment for genetically modified crops: problem formulation for stress tolerant crops. Plant Physiol. 147: 494-502.
42. Pardo JM and Quintero FJ (2002) Plants and sodium ions: keeping company with the enemy. Genome Biol. 3: Reviews 1017.1-1017.4.
43. Pascale V, Balhadère P, and Talbot NJ (2001) PDE1 encodes a P-Type ATPase involved in appressorium-mediated plant infection by the rice blast fungus Magnaporthe grisea. Plant Cell 13: 1987-2004.
44. Petronczki M, Matos J, Mori S, Gregan J, Bogdanova A, Schwickart M, Mechtler K, Shirahige K, Zachariae W, and Nasmyth K (2006) Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1. Cell 126: 1049-1064.
45. Poulsen LR, López-Marqués RL, McDowell SC, Okkeri J, Licht D, Schulz A, Pomorski T, Harper JF, and Palmgrena MG (2008) The Arabidopsis P4-ATPase ALA3 localizes to the golgi and requires α β-subunit to function in lipid translocation and secretory vesicle formation. Plant Cell 20: 658-676.
46. Poulter NS, Vatovec S, and Franklin-Tong VE (2008) Microtubules are a target for self-incompatibility signaling in Papaver pollen. Plant Physiol. 146: 1358-1367.
47. Rains DW (1972) Salt transport by plants in relation to salinity. Annu. Rev. Plant Physiol. 23: 367-388.
48. Reddy AM, Reddy VS, Scheffler BE, Wienand U, and Reddy AR (2007) Novel transgenic rice overexpressing anthocyanidin syn-thase accumulates a mixture of flavonoids leading to an increased antioxidant potential. Metab. Eng. 9: 95-111.
49. Reijans M, Lascaris R, Groeneger AO, Wittenberg A, Wesselink E, Oeveren J, Wit E, Boorsma A, Voetdijk B, van der Spek H, et al. (2003) Quantitative comparison of cDNA-AFLP, microarrays, and GeneChip expression data in Saccharomyces cerevisiae. Genomics 82: 606-618.
50. Robinson LC, Hubbard EJA, Graves PR, DePaoli-Roach AA, Roach PJ, Kung C, Haas DW, Hagedorn CH, Goebl M, et al. (1992) Yeast casein kinase I homologues: an essential gene pair. Proc. Natl. Acad. Sci. USA 89: 28-32.
51. Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjolander K, Yoshioka H, et al. (2005) Functional analysis of Avr9/Cf-9 rapidly elicited genes identifies a protein kinase, ACIK1, that is essential for full Cf-9-dependent disease resistance in tomato. Plant Cell 17: 295-310.
52. Sanders D, Brownlee C, and Harper JF (1999) Communicating with calcium. Plant Cell 11: 691-706.
53. Seo YW, Jang CS, Johnson JW (2011) Development of AFLP and STS markers for identifying wheat-rye translocations possessing 2RL. Euphytica 121: 279-287
54. Schmitz-Linneweber C, and Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci. 13: 663-670.
55. Schweighofer A, Hirt H, and Meskiene I (2004) Plant PP2C phospha-tases: emerging functions in stress signaling. Trends Plant Sci. 9: 236-243
56. Schweighofer A, Kazanaviciute V, Scheikl E, Teige M, Doczi R, Hirt H, Schwanninger M, Kant M, Schuurink R, Mauch F, et al. (2007) The PP2C-type phosphatase AP2C1, which negatively regulates MPK4 and MPK6, modulates innate Immunity, jasmonic acid, and ethylene levels in Arabidopsis. Plant Cell 19: 2213-2224.
57. Shiu SH and Bleecker AB (2001) Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc. Natl. Acad. Sci. U.S.A. 98: 10763-10768.
58. Shiu SH and Bleecker AB (2003) Expansion of the receptor-like kin-ase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol. 132: 530-543
59. Su H, Golldack D, Zhao C, and Bohnert HJ (2002) The expression of HAK-type K+ transporters is regulated in response to salinity stress in common ice plant. Plant Physiol. 129: 1482-1493.
60. Sun B, Chen L, Cao W, Roth AF, and Davis NG (2004) The yeast casein kinase Yck3p is palmitoylated, then sorted to the vacuolar membrane with AP-3-dependent recognition of a YXXPhi adaptin sorting signal. Mol. Biol. Cell 15: 1397-1406.
61. Tripathi V, Parasuraman B, Laxmi A, and Chattopadhyay D (2009) CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plants. Plant J. 58: 778-790.
62. Vuylsteke M, Daele HVD, Vercauteren A, Zabeau M, and Kuiper M (2006) Genetic dissection of transcriptional regulation by cDNA-AFLP. Plant J. 45: 439-446.
63. Wang M, Yu DS, Guo X, Cui Y, Li X, Zhang J, Zhao L, Chang H, Hu S, Zhang C, et al. (2011) Casein kinase 1-Like 3 is required for abscisic acid regulation of seed germination, root growth, and gene expression in Arabidopsis. Afr. J. Biotech. 61: 13219-13229.
64. Wang XJ, Liu W, Chen XM, Tang CL, Dong YL, Ma JB, Huang XL, Wei GR, Han QM, Huang LL, et al. (2010) Differential gene expression in incompatible interaction between wheat and stripe rust fungus revealed by cDNA-AFLP and comparison to compatible interaction. BMC Plant Biol. 10:9.
65. Widodo JHP, Newbigin E, Tester M, Bacic A, and Roessner U (2009) Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance. J Exp. Bot. 60: 4089-4103.
66. Xue T, Wang D, Zhang S, Ehlting J, Ni F, Jakab S, Zheng C, and Zhong Y (2008) Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis. BMC Genomics 9:550.
67. Zsigmond L, Rigó G, Szarka A, Székely G, Ötvös K, Darula Z, Medzihradszky KF, Koncz C, Koncz Z, and Szabados L (2008) Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport. Plant Physiol. 146: 1721-1737