Abstract
Proteins with the A20/AN1 zinc-finger domain are present in all eukaryotes and are well characterized in animals, but little is known about their function in plants. Earlier, we have identified an A20/AN1 zinc-finger containing stress associated protein 1 gene (SAP1) in rice and validated its function in abiotic stress tolerance. In this study, genome-wide survey of genes encoding proteins possessing A20/AN1 zinc-finger, named SAP gene family, has been carried out in rice and Arabidopsis. The genomic distribution and gene architecture as well as domain structure and phylogenetic relationship of encoded proteins numbering 18 and 14 in rice and Arabidopsis, respectively, have been studied. Expression analysis of the rice SAP family was done to investigate their response under abiotic stress conditions. All the genes were inducible by one or the other abiotic stresses indicating that the OsSAP gene family is an important component of stress response in rice. Manipulation of their expression and identification of their superior alleles should help confer stress tolerance in target crops.
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Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, Guimil S, Dunn M, Luginbuhl P, Ellero C, Goff SA, Glazebrook J (2003) A network of rice genes associated with stress response and seed development. Proc Natl Acad Sci USA 100:4945–4950
Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:17–124
Dixit VM, Green S, Sarma V, Holzman LB, Wolf FW, O’Rourke K, Ward PA, Prochownik EV, Marks RM (1990) Tumor necrosis factor-alpha induction of novel gene products in human endothelial cells including a macrophage-specific chemotaxin. J Biol Chem 265:2973–2978
Duan W, Sun B, Li TW, Tan BJ, Lee MK, Teo TS (2000) Cloning and characterization of AWP1, a novel protein that associates with serine/threonine kinase PRK1 in vivo. Gene 256:113–121
Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755–763
Evans PC, Ovaa H, Hamon M, Kilshaw PE, Hamm S, Bauer S, Ploegh HL, Smith TS (2004) Zinc-finger protein A20, a regulator of inflammation and cell survival, has de-ubiquitinating activity. Biochem J 378:727–734
Haralampidis K, Milioni D, Rigas S, Hatzopoulos P (2002) Combinatorial interaction of cis elements specifies the expression of the Arabidopsis AtHsp90–1 gene. Plant Physiol 129:1138–1149
Heyninck K, Beyaert R (2005) A20 inhibits NF-κB activation by dual ubiquitin-editing functions. Trends Biochem Sci 30:1–4
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res 27:297–300
Hishiya A, Iemura S, Natsume T, Takayama S, Ikeda K, Watanabe K (2006) A novel ubiquitin-binding protein ZNF216 functioning in muscle atrophy. EMBO J 25:554–564
Huang J, Teng L, Li L, Liu T, Li L, Chen D, Xu LG, Zhai Z, Shu HB (2004) ZNF216 is an A20-like and IkappaB kinase gamma-interacting inhibitor of NFkappaB activation. J Biol Chem 279:16847–16853
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
Jiang C, Iu B, Singh J (1996) Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus. Plant Mol Biol 30:679–684
Lee EG, Boone DL, Chai S, Libby SL, Chien M, Lodolce JP, Ma A (2000) Failure to regulate TNF-induced NF-kappaB and cell death responses in A20-deficient mice. Science 289:2350–2354
Lee S, Tsai YC, Mattera R, Smith WJ, Kostelansky MS, Weissman AM, Bonifacino JS, Hurley JH (2006) Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nat Struct Mol Biol 13:264–271
Linnen JM, Bailey CP, Weeks DL (1993) Two related localized mRNAs from Xenopus laevis encode ubiquitin-like fusion proteins. Gene 128:181–188
Mukhopadhyay A, Vij S, Tyagi AK (2004) Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proc Natl Acad Sci USA 101:6309–6314
Ono A, Izawa T, Chua NH, Shimamoto K (1996) The rab16B promoter of rice contains two distinct abscisic acid-responsive elements. Plant Physiol 112:483–491
Opipari AWJr, Boguski MS, Dixit VM (1990) The A20 cDNA induced by tumor necrosis factor alpha encodes a novel type of zinc finger protein. J Biol Chem 265:14705–14708
Penengo L, Mapelli M, Murachelli AG, Confalonieri S, Magri L, Musacchio A, Di Fiore PP, Polo S, Schneider TR (2006) Crystal structure of the ubiquitin binding domains of Rabex-5 reveals two modes of interactions with ubiquitin. Cell 124:1183–1195
Scott DA, Greinwald JH Jr, Marietta JR, Drury S, Swiderski RE, Vinas A, DeAngelis MM, Carmi R, Ramesh A, Kraft ML, Elbedour K, Skworak AB, Friedman RA, Srikumari Srisailapathy CR, Verhoeven K, Van Camp G, Lovett M, Deininger Pl, Batzer MA, Morton CC, Keats BJ, Smith RJH, Sheffield VC (1998) Identification and mutation analysis of a cochlear-expressed, zinc finger protein gene at the DFNB7/11 and dn hearing-loss-loci on human chromosome 9q and mouse chromosome 19. Gene 215:461–469
Sharma YK, Hinojos CM, Mehdy MC (1992) cDNA cloning, structure and expression of a novel pathogenesis-related protein in bean. Mol Plant Microbe Interact 5:89–95
Shinozaki K, Yamaguchi-Shinozaki K, Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6:410–417
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
Tsukamoto S, Morita S, Hirano E, Yokoi H, Masumura T, Tanaka K (2005) A novel cis-element that is responsive to oxidative stress regulates three antioxidant defense genes in rice. Plant Physiol 137:317–327
Tyagi AK, Vij S, Saini N (2006) Functional genomics of stress tolerance. In: Rao KVM, Raghavendra AS, Reddy KJ (eds) Physiology and molecular biology of stress tolerance. Springer, Dordrecht, pp 301–334
Vij S, Gupta V, Kumar D, Vydianathan R, Raghuvanshi S, Khurana P, Khurana JP, Tyagi AK (2006) Decoding the rice genome. BioEssays 28:421–432
Wertz IE, O’Rourke KM, Zhou H, Eby M, Aravind L, Seshagiri S, Wu P, Wiesmann C, Baker R, Boone DL, Ma A, Koonin EV, Dixit VM (2004) De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signaling. Nature 430:694–699
Xiong L, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14:65–183
Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6:251–26
Zhu JK (2001) Cell signaling under salt, water and cold stresses. Curr Opin Plant Biol 4:401–406
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This work was financially supported by grants from the Department of Biotechnology (DBT), Government of India. SV acknowledges CSIR for the award of a research fellowship.
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Communicated by K. Shirasu.
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Vij, S., Tyagi, A.K. Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis . Mol Genet Genomics 276, 565–575 (2006). https://doi.org/10.1007/s00438-006-0165-1
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DOI: https://doi.org/10.1007/s00438-006-0165-1