Transcriptome of Arabidopsis leaf senescence

Plant, Cell and Environment

Volumn 27, Issue 5, 2004, Pages 521-549

  Guo, Y ^a,b   Cai, Z ^b,c   Gan, S ^a,b  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

^b UNIVERSITY OF KENTUCKY   (United States)

^c UNIVERSITY OF KENTUCKY   (United States)

Author keywords

Environmental cues; Expressed sequence tag (EST); Gene expression; Genomics; Nutrient recycling; Proteinase; Signal transduction; Transcription factor

Indexed keywords

SENESCENCE;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 1842462559     PISSN: 01407791     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-3040.2003.01158.x     Document Type: Article

References (70)

1. Aida M., Ishida T., Fukaki H., Fujisawa H. & Tasaka M. (1997) Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9, 841-857.
2. Asai T., Tena G., Plotnikova J., Willmann M.R., Chiu W.L., Gomez-Gomez L., Boller T., Ausubel F.M. & Sheen J. (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415, 977-983.
3. Audic S. & Claverie J.M. (1997) The significance of digital gene expression profiles. Genome Research 7, 986-995.
4. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. & Wheeler D.L. (2003) GenBank. Nucleic Acids Research 31, 23-27.
5. Bernhard W.R. & Matile P. (1994) Differential expression of glutamine synthetase genes during the senescence of Arabidopsis thaliana rosette leaves. Plant Science 98, 7-14.
6. Bhalerao R., Keskitalo J., Sterky F., et al. (2003) Gene expression in autumn leaves. Plant Physiology 131, 430-442.
7. Buchanan-Wollaston V. (1994) Isolation of cDNA clones for genes that are expressed during leaf senescence in Brassica napus. Identification of a gene encoding a senescence-specific metallothionein-like protein. Plant Physiology 105, 839-846.
8. Buchanan-Wollaston V. & Ainsworth C. (1997) Leaf senescence in Brassica napus: cloning of senescence related genes by subtractive hybridisation. Plant Molecular Biology 33, 821-834.
9. Buchanan-Wollaston V., Earl S., Harrison E., Mathas E., Navabpour S., Page T. & Pink D. (2003) The molecular analysis of leaf senescence - a genomics approach. Plant Biotechnology Journal 1, 3-22.
10. Butt A., Mousley C., Morris K., Beynon J., Can C., Holub E., Greenberg J.T. & Buchanan-Wollaston V. (1998) Differential expression of a senescence-enhanced metallothionein gene in Arabidopsis in response to isolates of Peronospora parasitica and Pseudomonas syringae. Plant Journal 16, 209-221.
11. Carvalho H., Pereira S., Sunkel C. & Salema R. (1992) Detection of cytosolic glutamine synthetase in leaves of Nicotiana tabacum L. by immunocytochemical methods. Plant Physiology 100, 1591-1594.
12. Cobbett C. & Goldsbrough P. (2002) Phytochelatins and metallothioneins: roles in heavy metal detoxification and homeostasis. Annual Review of Plant Biology 53, 159-182.
13. Coschigano K.T., Melo-Oliveira R., Lim J. & Coruzzi G.M. (1998) Arabidopsis gls mutants and distinct Fd-GOGAT genes. Implications for photorespiration and primary nitrogen assimilation. Plant Cell 10, 741-752.
14. Dixon D.P., Lapthorn A. & Edwards R. (2002) Plant glutathione transferases. Genome Biology 3, http://genomebiology.com/ 2002/3/3/reviews/3004.
15. Doelling J.H., Walker J.M., Friedman E.M., Thompson A.R. & Vierstra R.D. (2002) The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. Journal of Biological Chemistry 277, 33105-33114.
16. Drake R., John I., Farrell A., Cooper W., Schuch W. & Grierson D. (1996) Isolation and analysis of cDNAs encoding tomato cysteine proteases expressed during leaf senescence. Plant Molecular Biology 30, 755-767.
17. Edwards J.W., Walker E.L. & Coruzzi G.M. (1990) Cell-specific expression in transgenic plants reveals nonoverlapping roles for chloroplast and cytosolic glutamine synthetase. Proceedings of the National Academy of Sciences of the USA 87, 3459-3463.
18. Eulgem T., Rushton P.J., Robatzek S. & Somssich I.E. (2000) The WRKY superfamily of plant transcription factors. Trends in Plant Science 5, 199-206.
19. Fan L., Zheng S. & Wang X. (1997) Antisense suppression of phospholipase Da retards abscisic acid- and ethylene-promoted senescence of postharvest Arabidopsis leaves. Plant Cell 9, 2183-2196.
20. Frishman D., Mokrejs M., Kosykh D., et al. (2003) The PEDANT genome database. Nucleic Acids Research 31, 207-211.
21. Gan S. (2003) Mitotic and postmitotic senescence in plants. Science's SAGE KE, http://sageke.sciencemag.org/cgi/content/full/ sageke;2003/38/re7.
22. Gan S. & Amasino R.M. (1997) Making sense of senescence. Molecular genetic regulation and manipulation of leaf senescence. Plant Physiology 113, 313-319.
23. Gray W.M., Hellmann H., Dharmasiri S. & Estelle M. (2002) Role of the Arabidopsis RING-H2 protein RBX1 in RUB modification and SCF function. Plant Cell 14, 2137-2144.
24. Haft D.H., Selengut J.D. & White O. (2003) The TIGRFAMs database of protein families. Nucleic Acids Research 31, 371-373.
25. Hajouj T., Michelis R. & Gepstein S. (2000) Cloning and characterization of a receptor-like protein kinase gene associated with senescence. Plant Physiology 124, 1305-1314.
26. Hanaoka H., Noda T., Shirano Y., Kato T., Hayashi H., Shibata D., Tabata S. & Ohsumi Y. (2002) Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiology 129, 1181-1193.
27. He Y. & Gan S. (2002) A gene encoding an acyl hydrolase is involved in leaf senescence in Arabidopsis. Plant Cell 14, 805-815.
28. He Y. & Gan S. (2003) Molecular characteristics of leaf senescence. In Recent Research Developments in Plant Molecular Biology, Vol. 1, pp. 1-17. Research Signpost, Kerala, India.
29. He Y., Fukushige H., Hildebrand D.F. & Gan S. (2002) Evidence supporting a role of jasmonic acid in Arabidopsis leaf senescence. Plant Physiology 128, 876-884.
30. He Y., Tang W., Swain J.D., Green A.L., Jack T.P. & Gan S. (2001) Networking senescence-regulating pathways by using Arabidopsis enhancer trap lines. Plant Physiology 126, 707-716.
31. Hensel L.L., Grbic V., Baumgarten D.A. & Bleecker A.B. (1993) Developmental and age-related processes that influence the longevity and senescence of photosynthetic tissues in Arabidopsis. Plant Cell 5, 553-564.
32. Himelblau E. & Amasino R.M. (2001) Nutrients mobilized from leaves of Arabidopsis thaliana during leaf senescence. Journal of Plant Physiology 158, 1317-1323.
33. Hinderhofer K. & Zentgraf U. (2001) Identification of a transcription factor specifically expressed at the onset of leaf senescence. Planta 213, 469-473.
34. Hortensteiner S. & Feller U. (2002) Nitrogen metabolism and remobilization during senescence. Journal of Experimental Botany 53, 927-937.
35. Ichimura K., Shinozaki K., Tena G., et al. (2002) Mitogen-activated protein kinase cascades in plants: a new nomenclature. Trends in Plant Science 7, 301-308.
36. Initiative T.A.G. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
37. Jepson I., Lay V.J., Holt D.C., Bright S.W. & Greenland A.J. (1994) Cloning and characterization of maize herbicide safener-induced cDNAs encoding subunits of glutathione S-transferase isoforms I, II and IV. Plant Molecular Biology 26, 1855-1866.
38. Jiang C.Z., Rodermel S.R. & Shibles R.M. (1993) Photosynthesis, Rubisco activity and amount, and their regulation by transcription in senescing soybean leaves. Plant Physiology 101, 105-112.
39. Joazeiro C.A. & Weissman A.M. (2000) RING finger proteins: mediators of ubiquitin ligase activity. Cell 102, 549-552.
40. Kamachi K., Yamaya T., Hayakawa T., Mae T. & Ojima K. (1992) Vascular bundle-specific localization of cytosolic glutamine synthetase in rice leaves. Plant Physiology 99, 1481-1486.
41. Kerk D., Bulgrien J., Smith D.W., Barsam B., Veretnik S. & Gribskov M. (2002) The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis. Plant Physiology 129, 908-925.
42. Komine Y., Kikis E., Schuster G. & Stern D. (2002) Evidence for in vivo modulation of chloroplast RNA stability by 3′-UTR homopolymeric tails in Chlamydomonas reinhardtii. Proceedings of the National Academy of Sciences of the USA 99, 4085-4090.
43. Komine Y., Kwong L., Anguera M.C., Schuster G. & Stern D.B. (2000) Polyadenylation of three classes of chloroplast RNA in Chlamydomonas reinhadtii. RNA 6, 598-607.
44. Lancien M., Martin M., Hsieh M.H., Leustek T., Goodman H. & Coruzzi G.M. (2002) Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway. Plant Journal 29, 347-358.
45. Lers A., Khalchitski A., Lomaniec E., Burd S. & Green P. (1998) Senescence-induced RNases in tomato. Plant Molecular Biology 36, 439-449.
46. Lim P.O., Woo H.R. & Nam H.G. (2003) Molecular genetics of leaf senescence in Arabidopsis. Trends in Plant Science 8, 272-278.
47. Liu L., White M.J. & MacRae T.H. (1999) Transcription factors and their genes in higher plants functional domains, evolution and regulation. European Journal of Biochemistry 262, 247-257.
48. Lohman K.N., Gan S., John M.C. & Amasino R.M. (1994) Molecular analysis of natural leaf senescence in Arabidopsis thaliana. Physiologia Plantarum 92, 322-328.
49. Morris K., MacKerness S.A., Page T., John C.F., Murphy A.M., Carr J.P. & Buchanan-Wollaston V. (2000) Salicylic acid has a role in regulating gene expression during leaf senescence. Plant Journal 23, 677-685.
50. Nicholson D.W. & Thornberry N.A. (1997) Caspases: killer proteases. Trends in Biochemistry and Science 22, 299-306.
51. Noodén L.D. (1988) Whole plant senescence. In Senescence and Aging in Plants (eds L.D. Noodén & A.C. Leopold), pp. 391-439. Academic Press, San Diego, CA, USA.
52. Ohlrogge J. & Benning C. (2000) Unraveling plant metabolism by EST analysis. Current Opinion in Plant Biology 3, 224-228.
53. Oliveira I.C., Brears T., Knight T.J., Clark A. & Coruzzi G.M. (2002) Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration. Plant Physiology 129, 1170-1180.
54. Quirino B.F., Normanly J. & Amasino R.M. (1999) Diverse range of gene activity during Arabidopsis thaliana leaf senescence includes pathogen-independent induction of defense-related genes. Plant Molecular Biology 40, 267-278.
55. Rhee S.Y., Beavis W., Berardini T.Z., et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 31, 224-228.
56. Riechmann J.L. & Ratcliffe O.J. (2000) A genomic perspective on plant transcription factors. Current Opinion in Plant Biology 3, 423-434.
57. Riechmann J.L., Heard J., Martin G., et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290, 2105-2110.
58. Robatzek S. & Somssich I.E. (2001) A new member of the Arabidopsis WRKY transcription factor family, AtWRKY6, is associated with both senescence- and defence-related processes. Plant Journal 28, 123-133.
59. Robatzek S. & Somssich I.E. (2002) Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Gene Development 16, 1139-1149.
60. Saedler H., Becker A., Winter K.U., Kirchner C. & Theissen G. (2001) MADS-box genes are involved in floral development and evolution. Acta Biochemica Pologica 48, 351-358.
61. Sambrook J. & Russell D.W. (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
62. Schoof H., Zaccaria P., Gundlach H., Lemcke K., Rudd S., Kolesov G., Arnold R., Mewes H.W. & Mayer K.F. (2002) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Research 30, 91-93.
63. Seki M., Narusaka M., Kamiya A., et al., (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296, 141-145.
64. Shiu S.H. & Bleecker A.B. (2001) Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proceedings of the National Academy of Sciences of the USA 98, 10763-10768.
65. Smart C.M., Hosken S.E., Thomas H., Greaves J.A., Blair B.G. & Schuch W. (1995) The timing of maize leaf senescence and characterization of senescence-related cDNAs. Physiologia Plantarum 93, 673-682.
66. Solomon M., Belenghi B., Delledonne M., Menachem E. & Levine A. (1999) The involvement of cysteine proteases and protease inhibitor genes in the regulation of programmed cell death in plants. Plant Cell 11, 431-444.
67. Stanton L.W. (2001) Methods to profile gene expression. Trends in Cardiovascular Medicine 11, 49-54.
68. Vernoud V., Horton A.C., Yang Z. & Nielsen E. (2003) Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiology 131, 1191-1208.
69. Wheeler D.L., Church D.M., Federhen S., et al. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Research 31, 28-33.
70. Yu D., Chen C. & Chen Z. (2001) Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression. Plant Cell 13, 1527-1540.