Using Specialized cDNA Microarrays to Analyze Arabidopsis Gene Expression Under Cold Stress

다국어 초록 (Multilingual Abstract)

Cold acclimation enables plants to withstand low but non-freezing temperatures. Biochemical and physiological changes include a reduction in tissue water content and altered composition of membrane lipids. These responses are correlated with fluctuations in the expression of coldinduced genes such as LTI (low-temperature-induced), KIN (cold-inducible), RD (responsive to desiccation), and ERD (early dehydration-inducible). We performed time-course experiments with specialized cDNA microarrays comprising 712 cDNAs selected by SAGE and SSH methods.
Expression dynamics were monitored in the leaves of Arabidopsis. Profiles of nine samples from plants chilled for various time periods revealed 264 cold-inducible genes and 33 repressed genes, for which expression was altered (up or down) by at least twofold. These included not only several previously reported cold-regulated genes, e.g., rd,lea, and CBF3, but also candidate genes such as those for alcohol dehydrogenase and transport inhibitor response 1.
All genes were grouped according to their expression patterns;most tended to shift their expression at 3∼8 h after cold treatment. Two cold-associated transcriptional activators,CBF2 and CBF3, did not have parallel patterns of expression,although both were induced within 15 min. Our results suggest different roles for CBF2 and CBF3 in the signaltransduction pathway for cold acclimation. We believe that,compared with standard differential screening, our microarray analysis is a more useful technique for the selection of new candidate genes responsible for cold acclimation.

참고문헌 (Reference)

1 Liu Q, 10 : 1391-1406, 1998

2 Gilmour SJ, "cDNA sequence analysis and expression of two cold-related genes of Arabidopsis thaliana" 18 : 13-22, 1992

3 Kreps JA, "Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress" 130 : 2129-2141, 2002

4 Hincha DK, "The role of sugar accumulation in leaf frost hardiness: investigations with transgenic tobacco expressing a bacterial pyrophosphatase or a yeast invertase gene" 174 : 604-610, 1996

5 Ingram J, "The molecular basis of dehydration tolerance in plants" 47 : 377-403, 1996

6 Iwasaki T, "The dehydration-inducible RD17 (Cor 47) gene and its promoter region in Arabidopsis thaliana (accession no. AB004872) (PGR 97-156)" 115 : 1287-, 1997

7 Baker SS, "The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought-, and ABA-regulated gene expression" 24 : 701-713, 1994

8 Anderson JV, "Structural organization of the spinach endoplasmic reticulumluminal 70-kilodalton heat-shock genes during cold acclimation" 104 : 1359-1370, 1994

9 Strauss G, "Stabilization of lipid bilayer vesicles by sucrose during freezing" 83 : 2422-2426, 1986

10 Koster KL, "Solute accumulation and compartmentation during the cold acclimation of Puma rye" 98 : 108-113, 1992

11 Thomashow MF, "So what’s new in the field of plant cold acclimation?" 125 : 89-93, 2001

12 Nordin K, "Separate signal pathways regulate the expression of a low-temperature-induced gene in Arabidopsis thaliana (L.) Heynh" 16 : 1061-1071, 1991

13 Nomura K, "Separate signal pathways regulate the expression of a low-temperature-induced gene in Arabidopsis thaliana (L.) Heynh" 16 : 1061-1071, 1991

14 Jaglo-Ottosen KR, "Science" 280 : 104-106, 1998

15 Steponkus PL, "Role of the plasma membrane in freezing injury and cold acclimation" 35 : 543-584, 1984

16 Thomashow MF, "Role of cold-responsive genes in plant freezing tolerance" 118 : 1-7, 1998

17 Mantyla E, "Role of abscisic acid in droughtinduced freezing tolerance, cold acclimation, and accumulation of LTI78 and RAB18 proteins in Arabidopsis thaliana" 107 : 141-148, 1995

18 Levitt J, "Responses of plants to environmental stresses, Vol 1, 2nd edn" Academic 1980

19 Schena M, "Quantitative monitoring of gene expression patterns with a complementary DNA microarray" 270 : 467-470, 1995

20 Wang H, "Promoters from Kin1 and cor6.6, two homologous Arabidopsis thaliana genes: transcriptional regulation of gene expression induced by low temperature, ABA osmoticum and dehydration" 28 : 605-617, 1995

21 Lynch DV, "Plasma membrane lipid alterations associated with cold acclimation of winter rye seedlings (Secale cereale L. cv Puma)" 83 : 761-767, 1987

22 Thomashow MF, "Plant cold acclimation: freezing tolerance genes and regulatory mechanisms" 50 : 571-599, 1999

23 Seki M, "Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray" 31 : 279-292, 2002

24 Seki M, "Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray" 13 : 61-72, 2001

25 Murelli C, "Metabolic changes associated with cold-acclimation in contrasting cultivars of barley" 94 : 87-93, 1995

26 Steponkus PL, "Membrane destabilization during freeze-induced dehydration" 10 : 37-47, 1993

27 Monroy AF, "Low-temperature signal transduction: induction of cold acclimation-specific genes of alfalfa by calcium at 25 degrees C" 7 : 321-331, 1995

28 Hughes MA, "Low temperature treatment of barley plants causes altered gene expression in shoot meristems" 39 : 1461-1467, 1988

29 Gilmour SJ, "Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression" 16 : 433-442, 1998

30 Leyva A, "Low temperature induces the accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs of Arabidopsis thaliana in a light-dependent manner" 108 : 39-46, 1995

31 Jarillo JA, "Low temperature induces the accumulation of alcohol dehydrogenase mRNA in Arabidopsis thaliana, a chilling-tolerant plant" 101 : 833-837, 1993

32 Chen THH, "Involvement of abscisic acid in potato cold acclimation" 71 : 362-365, 1983

33 Lee ML, "Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations" 97 : 9834-9839, 2000

34 Shinozaki K, "Gene expression and signal transduction in water stress response" 115 : 327-334, 1997

35 Seki M, "Functional annotation of a full length Arabidopsis cDNA collection" 296 : 141-145, 2002

36 Chen W, "Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses" 14 : 559-574, 2002

37 Prasad TK, "Evidence for chilling-induced oxidative stress in maize seedlings and a regulatory role for hydrogen peroxidase" 6 : 65-74, 1994

38 Carpenter JF, "Cryoprotection of phosphofructokinase with organic solutes: characterization of enhanced protection in the presence of divalent cations" 250 : 505-512, 1986

39 Lineberger RD, "Cryoprotection by glucose, sucrose, and raffinose to chloroplast thylakoids [spinach leaves]" 65 : 298-304, 1980

40 Yoshiba Y, "Correlation between the induction of a gene for delta-1-pyrroline-5-carboxylate synthetase and the accumulation of proline in Arabidopsis thaliana under osmotic stress" 7 : 751-760, 1995

41 Xin Z, "Cold comfort farm: the acclimation of plants to freezing temperatures" 23 : 893-902, 2000

42 Knight H, "Cold calcium signaling in Arabidopsis involved two cellular pools and a change in calcium signature after acclimation" 8 : 489-503, 1996

43 Uemura M, "Cold acclimation of Arabidopsis thaliana. Effect on plasma membrane lipid composition and freeze-induced lesions" 109 : 15-30, 1995

44 Gilmour SJ, "Cold acclimation and coldregulated gene expression in ABA mutants of Arabidopsis thaliana" 17 : 1223-1240, 1991

45 Gibson S, "Cloning of a temperature-regulated gene encoding a chloroplast omega-3 desaturase from Arabidopsis thaliana" 106 : 1615-1621, 1994

46 Kurkela S, "Cloning and characterization of a cold- and ABA-inducible Arabidopsis gene" 15 : 137-144, 1990

47 Welin BV, "Characterization and differential expression of dhn/lea/rab-like genes during cold acclimation and drought stress in Arabidopsis thaliana" 26 : 131-144, 1994

48 Zhu JK, "Cell signaling under salt, water and cold stresses" 4 : 401-406, 2001

49 Sheen J, "Ca-2+-dependent protein kinase and stress signal transduction in plants" 274 : 1900-1902, 1996

50 Shaffer MA, "Analysis of mRNAs that accumulate in response to low temperature identifies a thiol protease gene in tomato" 87 : 431-436, 1988

51 Guy CL, "Altered gene expression during cold acclimation of spinach" 83 : 3673-3677, 1985

52 Lang V, "Alterations in water status, endogenous abscisic acid content, and expression of rab18 gene during the development of freezing tolerance in Arabidopsis thaliana" 104 : 1341-1349, 1994

53 Ukaji N, "Accumulation of small heat-shock protein homologs in the endoplasmic reticulum of cortical parenchyma cells in mulberry in association with seasonal cold acclimation" 120 : 481-490, 1999

54 Kishitani S, "Accumulation of glycinebetaine during cold acclimation and freezing tolerance in leaves of winter and spring barley plants" 17 : 89-95, 1994

55 Heino P, "Abscisic acid deficiency prevents development of freezing tolerance in Arabidopsis thaliana (L.)" 79 : 801-806, 1990

56 Dunn MA, "A low temperature-responsive translation elongation factor 1 alpha from barley (Hordeum vulgare L.)" 23 : 221-225, 1993

57 Uemura M, "A contrast of the plasma membrane lipid composition of oat and rye leaves in relation to freezing tolerance" 104 : 479-496, 1994

58 Anderson JV, "A cDNA encoding the endoplasmic reticulum-luminal heat-shock protein from spinach (Spinacia oleracea L.)" 104 : 303-304, 1994