Differentially expressed genes under cold acclimation in Physcomitrella patens

Journal of Biochemistry and Molecular Biology

Volumn 40, Issue 6, 2007, Pages 986-1001

  Sun, Ming Ming ^a   Li, Lin Hui ^b   Xie, Hua ^c   Ma, Rong Cai ^c   He, Yi Kun ^a  

^a CAPITAL NORMAL UNIVERSITY   (China)

^b CHINA WEST NORMAL UNIVERSITY   (China)

^c Beijing Agro biotechnology Research Center   (China)

Author keywords

cDNA amplified fragment length polymorphism (cDNA AFLP); Cold acclimation; Gene expression profile; Physcomitrella patens (Hedw.); Real time RT PCR; Suppression subtractive hybridization (SSH)

Indexed keywords

BRYOPHYTA; BRYOPHYTES; EMBRYOPHYTA; PHYSCOMITRELLA; PHYSCOMITRELLA PATENS;

EID: 36949023148     PISSN: 12258687     EISSN: 02191024     Source Type: Journal    
DOI: 10.5483/bmbrep.2007.40.6.986     Document Type: Article

References (66)

1. Agulnick, A. D., Taira, M., Breen, J. J., Tanaka, T., Dawid, I. B. and Westphal, H. (1996) Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins. Nature 384, 270-272.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Ashton, N. W., Cove, D. J. and Featherstone, D. R. (1979) The isolation and physiological analysis of mutants of the moss Physcomitrella patens, which over-produce gametophores. Planta 144, 437-442.
4. Bachem, W. B., Oomen, F. J. and Visser, G. F. (1998) Transcript Imaging with cDNA-AFLP: a step-by-step protocol. Plant Mol. Biol. Rep. 16, 157-173.
5. Bahn, S. C., Bae, M. S., Park, Y. B., Oh, S. I., Jeung, J. U., Bae, J. M., Chung, Y. S. and Shin, J. S. (2001) Molecular cloning and characterization of a novel low temperature-induced gene, blti2, from barley (Hordeum vulgare L.). Biochim. Biophy. Acta 1522, 134-137.
6. Barret, P., Brinkman, M., Dufour, P., Murigneux, A. and Beckert, M. (2004) Identification of candidate genes for in vitro androgenesis induction in maize. Theor. Appl. Genet. 109, 1660-1668.
7. Bishop, G. J. and Koncz, C. (2002) Brassinosteroids and plant steroid hormone signaling. Plant Cell 14, 97-110.
8. Cove, D. (2005) The moss Physcomitrella patens. Ann. Rev. Genet. 39, 339-358.
9. Cove, D., Bezanilla, M., Harries, P. and Quatrano, R. (2006) Mosses as model systems for the study of metabolism and development. Annu. Rev. Plant Biol. 57, 497-520.
10. Feiler, H. S., Desprez, T., Santoni, V., Kronenberger, J., Caboche, M. and Traas, J. (1995) The higher plant Arabidopsis thaliana encodes a functional CDC48 homologue which is highly expressed in dividing and expanding cells. EMBO J. 14, 5626-5637.
11. Feinberg, A. P. and Vogelstein, B. (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132, 6-13.
12. Fowler, S. and Thomashow, M. F. (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.
13. Fujioka, S. and Sakurai, A. (1997) Brassinosteroids. Nat. Prod. Rep. 14, 1-10.
14. Gilmour, S. J., Sebolt, A. M., Salazar, M. P., Everard, J. D. and Thomashow, M. F. (2000) Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiol. 124, 1854-1865.
15. Gilmour, S. J., Zarka, D. G., Stockinger, E. J., Salazar, M. P., Houghton, J. M. and Thomashow, M. F. (1998) Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 16, 433-442.
16. Hall, Q. and Cannon, M. C. (2002) The cell wall hydroxyproline-rich glycoprotein RSH Is essential for normal embryo development in Arabidopsis. Plant Cell 14, 1161-1172.
17. He, J. X., Gendron, J. M., Yang, Y., Li, J. and Wang, Z. Y. (2002) The GSK3-like kinase BIN2 phosphorylates and destabilizes BZR1, a positive regulator of the brassinosteroid signaling pathway in Arabidopsis. Proc. Natl. Acad. Sci. USA 99, 10185-10190.
18. Hitz, W. D., Carlson, T. J., Booth, J. J., Kinney, A. J., Stecca, K. L. and Yadav, N. S. (1994) Cloning of a higher-plant plastid ù-6 fatty acid desaturase cDNA and Its expression in a Cyanobacterium. Plant Physiol. 105, 635-641.
19. Khan, S., Situ, G., Decker, K. and Schmidt, C. J. (2003) GoFigure: automated gene ontology™ annotation. Bioinformatics 19, 2484-2485.
20. Kinoshita, T., Cano-Delgado, A., Seto, H., Hiranuma, S., Fujioka, S., Yoshida, S. and Chory, J. (2005) Binding of brassinosteroids to the extracellular domain of plant receptor kinase BRI1. Nature 433, 167-171.
21. Knight, H., Trewavas, A. J. and Knight, M. R. (1996) Cold calcium signaling in Arabidopsis involves two cellular pools and a change in calcium signature after acclimation. Plant Cell 8, 489-503.
22. Kobayashi, F., Takumi, S., Nakata, M., Ohno, R., Nakamura, T. and Nakamura, C. (2004) Comparative study of the expression profiles of the Cor/Lea gene family in two wheat cultivars with contrasting levels of freezing tolerance. Physiol. Plant. 120, 585-594.
23. Krishna, P. (2003) Brassinosteroid-mediated stress responses. J. Plant Growth Regul. 22, 289-297.
24. Kroemer, K., Reski, R. and Frank, W. (2004) Abiotic stress response in the moss Physcomitrella patens: evidence for an evolutionary alteration in signaling pathways in land plants. Plant Cell Rep. 22, 864-870.
25. Kubien, D. S., Von Caemmerer, S., Furbank, R. T. and Sage, R. F. (2003) C4 photosynthesis at low temperature. A study using transgenic plants with reduced amounts of Rubisco. Plant Physiol. 132, 1577-1585.
26. Latowski, D., Kruk, J., Burda, K., Skrzynecka-Jaskier, M., Kostecka-Gugala, A. and Strzalka, K. (2002) Kinetics of violaxanthin de-epoxidation by violaxanthin de-epoxidase, a xanthophy cycle enzyme, is regulated by membrane fluidity in model lipid bilayers. Euro. J. Biochem. 269, 4656-4665.
27. Lee, B. H., Henderson, D. A. and Zhu, J. K. (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell 17, 3155-3175.
28. Li, J., Nam, K. H., Vafeados, D. and Chory, J. (2001) BIN2, a new brassinosteroid-insensitive locus in Arabidopsis. Plant Physiol. 127, 14-22.
29. Lin, W. H., Ye, R., Ma, H., Xu , Z. H. and Xue, H. W. (2004) DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments. Cell Res. 14, 34-45.
30. Lindemann, P., Koch, A., Degenhardt, B., Hause, G., Grimm, B. and Papadopoulos, V. (2004) A novel Arabidopsis thaliana protein is a functional peripheral-type benzodiazepine receptor. Plant Cell Physiol. 45, 723-733.
31. Liu, N., Zhong, N. Q., Wang, G. L., Li, L. J., Liu, X. L., He, Y. K. and Xia, G. X. (2007) Cloning and functional characterization of PpDBF1 gene encoding a DRE-binding transcription factor from Physcomitrella patens. Planta 226, 827-838
32. Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K. and Shinozaki, K. (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10, 1391-1406.
33. Livingston, D. P. III. and Henson, C. A. (1998) Apoplastic sugars, fructans, fructan exohydrolase, and invertase in winter oat: responses to second-phase cold-hardening. Plant Physiol. 116, 403-408.
34. McCarter, J. P., Mitreva, M. D., Martin, J., Dante, M., Wylie, T., Rao, U., Pape, D., Bowers, Y., Theising, B., Murphy, C. V., Kloek, A. P., Chiapelli, B. J., Clifton, S. W., Bird, D. M. and Waterston, R. H. (2003) Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 4, 26-44.
35. Minami, A., Nagao, M., Arakawa, K., Fujikawa, S. and Takezawa, D. (2003) Abscisic acid-induced freezing tolerance in the moss Physcomitrella patens is accompanied by increased expression of stress-related genes. J. Plant Physiol. 160, 475-483.
36. Minami, A., Nagao, M., Ikegami, K., Koshiba, T., Arakawa, K., Fujikawa, S. and Takezawa, D. (2005) Cold acclimation in bryophytes: low-temperature- induced freezing tolerance in Physcomitrella patens is associated with increases in expression levels of stress-related genes but not with increase in level of endogenous abscisic acid. Planta 220, 414-423.
37. Miyoshi, K., Ahn, B. O., Kawakatsu, T., Ito, Y., Itoh, J. I., Nagato, Y. and Kurata, N. (2004) PLASTOCHRON1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. Proc. Nat. Acad. Sci. USA 101, 875-880.
38. Murata, N., Ishizaki-Nishizawa, O., Higashi, S., Hayashi, H., Tasaka, Y. and Nishida, I. (1992) Genetically engineered alteration in the chilling sensitivity of plants. Nature 356, 710-713.
39. Nishiyama, T., Fujita, T., Shin, T., Seki, M., Nishide, H., Uchiyama, I., Kamiya, A., Carninci, P., Hayashizaki, Y., Shinozaki, K., Kohara, Y. and Hasebe, M. (2003) Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolution. Proc. Nat. Acad. Sci. USA 100, 8007-8012.
40. Noguchi, T., Fujioka, S., Choe, S., Takatsuto, S., Tax, F. E., Yoshida, S. and Feldmann, K. A. (2000) Biosynthetic pathways of brassinolide in Arabidopsis. Plant Physiol. 124, 201-209.
41. Oldenhof, H., Wolkers, W. F., Bowman, J. L., Tablin, F. and Crowe, J. H. (2006) Freezing and desiccation tolerance in the moss Physcomitrella patens: an in situ fourier transform infrared spectroscopic study. Biochim. Biophys. Acta 1760, 1226-1234.
42. Pfaffl, M. W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, 45-50.
43. Quatrano, R. S., McDaniel, S. F., Khandelwal, A., Perroud, P. F. and Cove, D. J. (2007) Physcomitrella patens: mosses enter the genomic age. Curr. Opin. Plant Biol. 10, 182-189.
44. Rancour, D. M., Dickey, C. E., Park, S. and Bednarek, S. Y. (2002) Characterization of AtCDC48. Evidence for multiple membrane fusion mechanisms at the plane of cell division in plants. Plant Physiol. 130, 1241-1253.
45. Rancour, D. M., Park, S., Knight, S. D. and Bednarek, S. Y. (2004) Plant UBX domain-containing protein 1, PUX1, regulates the oligomeric structure and activity of Arabidopsis CDC48. J. Biol. Chem. 279, 54264-54274.
46. Rensing, S. A., Fritzowsky, D., Lang, D. and Reski, R. (2005) Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens. BMC Genomics 6, 43-56.
47. Robaglia, C., Bruening, G., Haseloff, J. and Gerlach, W. L. (1993) Evolution and replication of tobacco ringspot virus satellite RNA mutants. EMBO J. 12, 2969-2976.
48. Robinson, S. A., Wasley, J. and Tobin, A. K. (2003) Living on the edge-plants and global change in continental and maritime Antarctica. Global Change Biol. 9, 1681-1717.
49. Sablowski, R. and Harberd, N. P. (2005) Plant sciences. Plant genes on steroids. Science 307, 1569-1570.
50. Sambrook, J. and Russell, D. W. (2001) Molecular cloning: a laboratory manual. thrid ed. Cold Spring Harbor Laboratory Press, New York, USA.
51. Schaefer, D. G. and Zryd, J. P. (2001) The moss Physcomitrella patens, now and then. Plant Physiol. 127, 1430-1438.
52. Schmeichel, K. L. and Beckerle, M. C. (1994) The LIM domain is a modular protein-binding interface. Cell 79, 211-219.
53. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninic, P., Hayashizaki, Y. and Shinozaki, K. (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13, 61-72.
54. Stockinger, E. J., Gilmour, S. J. and Thomashow, M. F. (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, A cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Nat. Acad. Sci. USA 94, 1035-1040.
55. Taylor, I. B., Burbidage, A. and Thompson, A. J. (2000) Control of abscisic acid synthesis. J. Exp. Bot. 51, 1563-1574.
56. Thomashow, M. F. (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Ann. Rev. Plant Physiol. Plant Mol. Biol. 50, 571-599.
57. Thomashow, M. F. (2001) So what's new in the field of plant cold acclimation? Lots! Plant Physiol. 125, 89-93.
58. Wada, H., Gombos, Z. and Murata, N. (1990) Enhancement of chilling tolerance of a cyanobacterium by genetic manipulation of fatty acid desaturation. Nature 347, 200-203.
59. Welin, B. V., Olson, A. and Palva, E. T. (1995) Structure and organization of two closely related low-temperature-induced dhn/lea/rab-like genes in Arabidopsis thaliana L. Heynh. Plant Mol. Biol. 29, 391-395.
60. Wolter, F. P., Schmidt, R. and Heinz, E. (1992) Chilling sensitivity of Arabidopsis thaliana with genetically engineered membrane lipids. EMBO J. 11, 4685-4692.
61. Xiong, L. M., Schumaker, K. S. and Zhu, J. K. (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 165-183.
62. Xiong, L. M. and Zhu, J. K. (2001) Abiotic stress signal transduction in plants: Molecular and genetic perspectives. Physiol. Plant. 112, 152-166.
63. Yamaguchi-Shinozaki, K. and Shinozaki, K. (2006) Transcriptional regulatory networks in cellular response and the tolerance to dehydration and cold stresses. Annu. Rev. Plant Biol. 57, 781-803.
64. Yin, Y., Vafeados, D., Tao, Y., Yoshida, S. and Asami, T. C. J. (2005) A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell 120, 249-259.
65. Yin, Y., Wang, Z. Y., Mora-Garcia, S., Li, J., Yoshida, S., Asami, T. and Chory, J. (2002) BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Plant Cell 109, 181-191.
66. Yoshiba, Y., Aoki, C., Iuchi, S., Nanjo, T., Seki, M., Sekiguchi, F., Yamaguchi-Shinozaki, K. and Shinozaki, K. (2001) Characterization of four extensin genes in Arabidopsis thaliana by differential gene expression under stress and non-stress conditions. DNA Res. 8, 115-122.