Analysis of EF-hand-containing proteins in Arabidopsis

Genome Biology

Volumn 3, Issue 10, 2002, Pages

  Day, Irene S ^a   Reddy, Vaka S ^a   Shad Ali, Gul ^a   Reddy, Asn ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

Arabidopsis Genome; Mitochondrial Carrier Protein; Rboh; Respiratory Burst Oxidase; Respiratory Burst Oxidase Homology

Indexed keywords

ARABIDOPSIS PROTEIN; CALCIUM BINDING PROTEIN; SIGNAL PEPTIDE;

ARABIDOPSIS; ARTICLE; CHEMISTRY; GENETICS; METHODOLOGY; PHYLOGENY; PROTEIN DATABASE; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CALCIUM-BINDING PROTEINS; DATABASES, PROTEIN; EF HAND MOTIFS; PHYLOGENY; PROTEIN SORTING SIGNALS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN;

EID: 0037163398     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2002-3-10-research0056     Document Type: Article

References (83)

1. 2+ signaling in plant cells: the big network!. Curr Opin Plant Biol. 1998, 1: 428-433. 10.1016/S1369-5266(98)80268-9. DOI: 10.1016/S1369-5266(98)80268-9
2. Poovaiah BW, Reddy ASN: Calcium and signal transduction in plants. CRC Crit Rev Plant Sci. 1993, 12: 185-211. DOI: 10.1080/713608046
3. Reddy ASN: Calcium: silver bullet in signaling. Plant Sci. 2000, 160: 381-404. 10.1016/S0168-9452(00)00386-1. DOI: 10.1016/S0168-9452(00)00386-1
4. Zielinski RE: Calmodulin and calmodulin-binding proteins in plants. Annu Rev Pl Physiol Pl Mol Biol. 1998, 49: 697-725. 10.1146/annurev.arplant.49.1.697. DOI: 10.1146/annurev.arplant.49.1.697
5. White PJ: Calcium channels in higher plants. Biochim Biophys Acta. 2000, 1465: 171-189. 10.1016/S0005-2736(00)00137-1. DOI: 10.1016/S0005-2736(00)00137-1
6. Knight H: Calcium signaling during abiotic stress in plants. Int Rev Cytol. 2000, 195: 269-324. DOI: 10.1016/S0074-7696(08)62707-2
7. Reddy ASN, Reddy V: Calcium as a messenger in stress signal transduction. In: Handbook of Plant and Crop Physiology. Edited by: Pessarakali M. 2001, New York: Mercel Dekker, 697-732.
8. Snedden WA, Fromm H: Calmodulin, calmodulin-related proteins and plant responses to the environment. Trends Plant Sci. 1998, 3: 299-304. 10.1016/S1360-1385(98)01284-9. DOI: 10.1016/S1360-1385(98)01284-9
9. Roberts DM, Harmon AC: Calcium modulated proteins: targets of intracellular calcium signals in higher plants. Annu Rev Pl Physiol Pl Mol Biol. 1992, 43: 375-414. 10.1146/annurev.pp.43.060192.002111. DOI: 10.1146/annurev.pp.43.060192.002111
10. Kretsinger RH, Nockolds CE: Carp muscle calcium-binding protein. II. Structure determination and general description. J Biol Chem. 1973, 248: 3313-3326.
11. Nakayama S, Kawasaki H, Kretsinger R: Evolution of EF-hand proteins. In: Calcium Homeostasis. Edited by: Carafoli E, Krebs J. 2000, New York: Springer, 29-58. DOI: 10.1007/978-3-642-58306-3_2
12. 2+ exchange in parvalbumin and other EF-hand proteins. A theoretical study. J Mol Biol. 1999, 285: 857-73. 10.1006/jmbi.1998.2329. DOI: 10.1006/jmbi.1998.2329
13. Luan S, Kudla J, Rodriguez-Concepcion M, Yalovsky S, Gruissem W: Calmodulins and calcineurin B-like proteins: calcium sensors for specific signal response coupling in plants. Plant Cell. 2002, S389-S400. Suppl
14. Lewit-Bentley A, Rety S: EF-hand calcium-binding proteins. Curr Opin Struct Biol. 2000, 10: 637-643. 10.1016/S0959-440X(00)00142-1. DOI: 10.1016/S0959-440X(00)00142-1
15. Perera IY, Zielinski E: Structure and expression of the Arabidopsis CaM-3 calmodulin gene. Plant Mol Biol. 1992, 19: 649-664. DOI: 10.1007/BF00026791
16. Ling V, Perea I, Zielinski RE: Primary structures of Arabidopsis calmodulin isoforms deduced from the sequences of cDNA clones. Plant Physiol. 1991, 96: 1196-1212. DOI: 10.1104/pp.96.4.1196
17. Gawienowski MC, Szymanski D, Perera IY, Zielinski RE: Calmodulin isoforms in Arabidopsis encoded by multiple divergent mRNAs. Plant Mol Biol. 1993, 22: 215-25. DOI: 10.1007/BF00014930
18. Zielinski RE: Characterization of three new members of the Arabidopsis thaliana calmodulin gene family: conserved and highly diverged members of the gene family functionally complement a yeast calmodulin null. Planta. 2002, 214: 446-455. 10.1007/s004250100636. DOI: 10.1007/s004250100636
19. Ling V, Zielinski RE: Isolation of an Arabidopsis cDNA sequence encoding a 22 kDa calcium-binding protein (CaBP-22) related to calmodulin. Plant Mol Biol. 1993, 22: 207-214. DOI: 10.1007/BF00014929
20. Braam J, Davis RW: Rain-, wind-, and touch-induced expression of calmodulin and calmodulin-related genes in Arabidopsis. Cell. 1990, 60: 357-364. DOI: 10.1016/0092-8674(90)90587-5
21. Cordeiro MC, Piqueras R, de Oliveira DE, Castresana C: Characterization of early induced genes in Arabidopsis thaliana responding to bacterial inoculation: identification of centrin and of a novel protein with two regions related to kinase domains. FEBS Lett. 1998, 434: 387-393. 10.1016/S0014-5793(98)01015-1. DOI: 10.1016/S0014-5793(98)01015-1
22. 2+ signal?. Trends Plant Sci. 2000, 5: 154-159. 10.1016/S1360-1385(00)01577-6. DOI: 10.1016/S1360-1385(00)01577-6
23. Kudla J, Xu Q, Harter K, Gruissem W, Luan S: Genes for calcineurin B-like proteins in Arabidopsis are differentially regulated by stress signals. Proc Natl Acad Sci USA. 1999, 96: 4718-4123. 10.1073/pnas.96.8.4718. DOI: 10.1073/pnas.96.8.4718
24. Liu J, Zhu JK: A calcium sensor homolog required for plant salt tolerance. Science. 1998, 280: 1943-1945. 10.1126/science.280.5371.1943. DOI: 10.1126/science.280.5371.1943
25. McCurdy DW, Kim M: Molecular cloning of a novel fimbrin-like cDNA from Arabidopsis thaliana. Plant Mol Biol. 1998, 36: 23-31. 10.1023/A:1005884112192. DOI: 10.1023/A:1005884112192
26. phox). Plant J. 1998, 14: 365-370. 10.1046/j.1365-313X.1998.00136.x. DOI: 10.1046/j.1365-313X.1998.00136.x
27. 2+ binding motifs. Plant Cell. 1998, 10: 255-266. 10.1105/tpc.10.2.255.
28. Hirayama T, Mitsukawa N, Shibata D, Shinozaki K: AtPLC2, a gene encoding phosphoinositide-specific phospholipase C, is constitutively expressed in vegetative and floral tissues in Arabidopsis thaliana. Plant Mol Biol. 1997, 34: 175-180. 10.1023/A:1005885230896. DOI: 10.1023/A:1005885230896
29. Otterhag L, Sommarin M, Pical C: N-terminal EF-hand-like domain is required for phosphoinositide-specific phospholipase C activity in Arabidopsis thaliana. FEBS Lett. 2001, 497: 165-170. 10.1016/S0014-5793(01)02453-X. DOI: 10.1016/S0014-5793(01)02453-X
30. 2+ flux in Arabidopsis leaf cells. Plant Cell Physiol. 2001, 42: 900-905. 10.1093/pcp/pce145. DOI: 10.1093/pcp/pce145
31. 2+ dependency. EMBO J. 1997, 16: 2565-2575. 10.1093/emboj/16.10.2565. DOI: 10.1093/emboj/16.10.2565
32. Turano FJ, Thakkar SS, Fang T, Weisemann JM: Characterization and expression of NAD(H)-dependent glutamate dehydrogenase genes in Arabidopsis. Plant Physiol. 1997, 113: 1329-1341. 10.1104/pp.113.4.1329. DOI: 10.1104/pp.113.4.1329
33. Leung J, Bouvier-Durand M, Morris PC, Guerrier D, Chefdor F, Giraudat J: Arabidopsis ABA response gene ABI1: features of a calcium-modulated protein phosphatase. Science. 1994, 264: 1448-1452. DOI: 10.1126/science.7910981
34. Meyer K, Leube MP, Grill E: A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana. Science. 1994, 264: 1452-1455. DOI: 10.1126/science.8197457
35. 2+-binding protein that is induced by NaCl stress. Plant Mol Biol. 1998, 37: 839-847. 10.1023/A:1006043006211. DOI: 10.1023/A:1006043006211
36. Rozwadowski K, Zhao R, Jackman L, Huebert T, Burkhart WE, Hemmingsen SM, Greenwood J, Rothstein SJ: Characterization and immunolocalization of a cytosolic calcium-binding protein from Brassica napus and Arabidopsis pollen. Plant Physiol. 1999, 120: 787-798. 10.1104/pp.120.3.787. DOI: 10.1104/pp.120.3.787
37. The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 408: 796-815. 10.1038/35048692. DOI: 10.1038/35048692
38. Munich Information Center for Protein Sequences. [http://www.mips.biochem.mpg.de]
39. Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer KF: MIPS Arabidopsis thaliana database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 2002, 30: 91-93. 10.1093/nar/30.1.91. DOI: 10.1093/nar/30.1.91
40. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001, 29: 37-40. 10.1093/nar/29.1.37. DOI: 10.1093/nar/29.1.37
41. Mulder NJ, Apweiler R: Tools and resources for identifying protein families, domains and motifs. Genome Biol. 2002, 3: 1-2001.
42. Hirayama T, Ohto C, Mizoguchi T, Shinozaki K: A gene encoding a phosphatidylinositol-specific phospholipase C is induced by dehydration and salt stress in Arabidopsis thaliana. Proc Natl Acad Sci USA. 1995, 92: 3903-3907. DOI: 10.1073/pnas.92.9.3903
43. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al: The sequence of the human genome. Science. 2001, 291: 1304-1351. 10.1126/science.1058040. DOI: 10.1126/science.1058040
44. TargetP v1.01. [http://www.cbs.dtu.dk/services/TargetP/]
45. Frandsen G, Muller-Uri F, Nielsen M, Mundy J, Skriver K: Novel plant Ca(2+)-binding protein expressed in response to abscisic acid and osmotic stress. J Biol Chem. 1996, 271: 343-348. 10.1074/jbc.271.1.343. DOI: 10.1074/jbc.271.1.343
46. 2+-binding proteins associated with lipid bodies. Plant Mol Biol. 2000, 44: 463-476. 10.1023/A:1026564411918. DOI: 10.1023/A:1026564411918
47. 2+-binding protein is induced by abscisic acid during dehydration. Plant Cell Physiol. 2000, 41: 898-903. 10.1093/pcp/pcd010. DOI: 10.1093/pcp/pcd010
48. Lu G, Sehnke PC, Ferl RJ: Phosphorylation and calcium binding properties of an Arabidopsis GF14 brain protein homolog. Plant Cell. 1994, 6: 501-510. 10.1105/tpc.6.4.501. DOI: 10.1105/tpc.6.4.501
49. Athwal GS, Huber S: Divalent cations and polyamines bind to loop 8 of 14-3-3 proteins, modulating their interaction with phosphorylated nitrate reductase. Plant J. 2002, 29: 119-129. 10.1046/j.0960-7412.2001.01200.x. DOI: 10.1046/j.0960-7412.2001.01200.x
50. 2+-binding protein involved in cryptochrome and phytochrome coaction. Science. 2002, 291: 487-490. 10.1126/science.291.5503.487. DOI: 10.1126/science.291.5503.487
51. Kovar DR, Staiger CJ, Weaver EA, McCurdy DW: AtFim1 is an actin filament crosslinking protein from Arabidopsis thaliana. Plant J. 2000, 24: 625-636. 10.1046/j.1365-313x.2000.00907.x. DOI: 10.1046/j.1365-313x.2000.00907.x
52. Guo Y, Halfter U, Ishitani M, Zhu JK: Molecular characterization of functional domains in the protein kinase SOS2 that is required for plant salt tolerance. Plant Cell. 2001, 13: 1383-1400. 10.1105/tpc.13.6.1383. DOI: 10.1105/tpc.13.6.1383
53. Halfter U, Ishitani M, Zhu JK: The Arabidopsis SOS2 protein kinase physically interacts with and is activated by the calcium-binding protein SOS3. Proc Natl Acad Sci USA. 2000, 97: 3735-3740. 10.1073/pnas.040577697. DOI: 10.1073/pnas.97.7.3735
54. Kim KN, Cheong YH, Gupta R, Luan S: Interaction specificity of Arabidopsis calcineurin B-like calcium sensors and their target kinases. Plant Physiol. 2000, 124: 1844-1853. 10.1104/pp.124.4.1844. DOI: 10.1104/pp.124.4.1844
55. 2+-regulated kinases. EMBO J. 2001, 20: 1051-1063. 10.1093/emboj/20.5.1051. DOI: 10.1093/emboj/20.5.1051
56. The Arabidopsis Functional Genomics Network. [http://www.bio.uni-frankfurt.de/botanik/mcb/AFGN/kudla.html]
57. Jakobek JL, Smith-Becker JA, Lindgren PB: A bean cDNA expressed during a hypersensitive reaction encodes a putative calcium-binding protein. Mol Plant Microbe Interact. 1999, 12: 712-719. DOI: 10.1094/MPMI.1999.12.8.712
58. Hendershot JD, Esmon CA, Lumb JE, Rundle SJ: Identification and characterization of sequences encoding a 62-kilodalton B' regulatory subunit of Arabidopsis protein phosphatase 2A. Plant Physiol. 1999, 121: 311-10.1104/pp.121.1.311. DOI: 10.1104/pp.121.1.311
59. Reddy ASN, Safadi F, Narasimhulu SB, Golovkin M, Hu X: A novel plant calmodulin-binding protein with a kinesin heavy chain motor domain. J Biol Chem. 1996, 271: 7052-7060. 10.1074/jbc.271.12.7052. DOI: 10.1074/jbc.271.12.7052
60. Reddy V, Safadi F, Zielinski RE, Reddy ASN: Interaction of a kinesin-like protein with calmodulin isoforms from Arabidopsis. J Biol Chem. 1999, 274: 31727-31733. 10.1074/jbc.274.44.31727. DOI: 10.1074/jbc.274.44.31727
61. 2+-binding protein in wheat cultured cells. Plant Mol Biol. 2000, 42: 807-817. 10.1023/A:1006431724090. DOI: 10.1023/A:1006431724090
62. O'Neil KT, DeGrado WF: How calmodulin binds its targets: sequence-independent recognition of amphiphilic α-helices. Trends Biochem Sci. 1990, 15: 59-64. 10.1016/0968-0004(90)90177-D. DOI: 10.1016/0968-0004(90)90177-D
63. Liao B, Gawienowski MC, Zielinski RE: Differential stimulation of NAD kinase and binding of peptide substrates by wild-type and mutant plant calmodulin isoforms. Arch Biochem Biophys. 1996, 327: 53-60. 10.1006/abbi.1996.0092. DOI: 10.1006/abbi.1996.0092
64. Bartling D, Butler H, Weiler EW: Arabidopsis thaliana cDNA encoding a novel member of the EF-hand superfamily of calcium-binding proteins. Plant Physiol. 1993, 102: 1059-1060. 10.1104/pp.102.3.1059. DOI: 10.1104/pp.102.3.1059
65. PlantsP. [http://plantsP.sdsc.edu]
66. Hrabak EM, Dickmann LJ, Satterlee JS, Sussman MR: Characterization of eight new members of the calmodulin-like domain protein kinase gene family from Arabidopsis thaliana. Plant Mol Biol. 1996, 31: 405-412. DOI: 10.1007/BF00021802
67. Hrabak E: Calcium-dependent protein kinases and their relatives. In: Advances in Botanical Research Incorporating Advances in Plant Pathology. Edited by: Krie M, Walker J. 2000, San Diego, CA: Academic Press, Inc, 32: 185-223.
68. Weljie AM, Clarke TE, Juffer AH, Harmon AC, Vogel HJ: Comparative modeling studies of the calmodulin-like domain of calcium-dependent protein kinase from soybean. Proteins. 2000, 39: 343-357. 10.1002/(SICI)1097-0134(20000601)39:4<343::AID-PROT70>3.0.CO;2-2. DOI: 10.1002/(SICI)1097-0134(20000601)39:4<343::AID-PROT70>3.0.CO;2-2
69. Hong Y, Takano M, Liu CM, Gasch A, Chye ML, Chua NH: Expression of three members of the calcium-dependent protein kinase gene family in Arabidopsis thaliana. Plant Mol Biol. 1996, 30: 1259-1275. DOI: 10.1007/BF00019557
70. 2+-dependent protein kinases are induced by drought and high-salt stresses in Arabidopsis thaliana. Mol Gen Genet. 1994, 244: 331-340. DOI: 10.1007/BF00286684
71. 2+-dependent protein kinase. Plant Physiol. 1994, 105: 1461-1462. 10.1104/pp.105.4.1461. DOI: 10.1104/pp.105.4.1461
72. Camoni L, Harper JF, Palmgren MG: 14-3-3 proteins activate a plant calcium-dependent protein kinase (CDPK). FEBS Lett. 1998, 430: 381-384. 10.1016/S0014-5793(98)00696-6. DOI: 10.1016/S0014-5793(98)00696-6
73. 2+ pump (ACA2) located in the endoplasmic reticulum of Arabidopsis. Proc Natl Acad Sci USA. 2000, 97: 6224-6229. 10.1073/pnas.97.11.6224. DOI: 10.1073/pnas.97.11.6224
74. 2+-dependent protein kinases and stress signal transduction in plants. Science. 1996, 274: 1900-1902. 10.1126/science.274.5294.1900. DOI: 10.1126/science.274.5294.1900
75. Tahtiharju S, Sangwan V, Monory AF, Dhindsa RS, Borg M: The induction of kin genes in cold-acclimating Arabidopsis thaliana: Evidence of a role for calcium. Planta. 1997, 203: 442-447. 10.1007/s004250050212. DOI: 10.1007/s004250050212
76. Johnson KD, Chrispeels MJ: Tonoplast-bound protein kinase phosphorylates tonoplast intrinsic protein. Plant Physiol. 1992, 100: 1787-1795. DOI: 10.1104/pp.100.4.1787
77. Lamb CJ, Dixon RA: The oxidative burst in plant disease resistance. Annu Rev Pl Physiol Pl Mol Biol. 1997, 48: 251-275. 10.1146/annurev.arplant.48.1.251. DOI: 10.1146/annurev.arplant.48.1.251
78. Leung J, Merlot S, Giraudat J: The Arabidopsis ABSCISIC ACID-INSENSITIVE2 (ABI2) and ABI1 genes encode homologous protein phosphatases 2C involved in abscisic acid signal transduction. Plant Cell. 1997, 9: 759-771. 10.1105/tpc.9.5.759. DOI: 10.1105/tpc.9.5.759
79. Trewavas A: Mindless mastery. Nature. 2002, 425: 841-10.1038/415841a. DOI: 10.1038/415841a
80. Reddy VS, Ali GS, Reddy ASN: Genes encoding calmodulin-binding proteins in the Arabidopsis genome. J Biol Chem. 2002, 277: 9840-9852. 10.1074/jbc.M111626200. DOI: 10.1074/jbc.M111626200
81. PubMed.[http://www.ncbi.nlm.nih.gov/PubMed/]
82. Romeis T, Piedras P, Jones JD: Resistance gene-dependent activation of a calcium-dependent protein kinase in the plant defense response. Plant Cell. 2000, 12: 803-816. 10.1105/tpc.12.5.803. DOI: 10.1105/tpc.12.5.803
83. Harper JF, Huang JF, Lloyd SJ: Genetic identification of an autoinhibitor in CDPK, a protein kinase with a calmodulin-like domain. Biochemistry. 1994, 33: 7267-7277. DOI: 10.1021/bi00189a031