Comprehensive expression analysis of rice armadillo gene family during abiotic stress and development

DNA Research

Volumn 21, Issue 3, 2014, Pages 267-283

  Sharma, Manisha ^a   Singh, Amarjeet ^a   Shankar, Alka ^a   Pandey, Amita ^a   Baranwal, Vinay ^a   Kapoor, Sanjay ^a   Tyagi, Akhilesh K ^a,b   Pandey, Girdhar K ^a  

^a UNIVERSITY OF DELHI   (India)

^b NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

abiotic stress; Armadillo; development; signal transduction

Indexed keywords

ARMADILLO DOMAIN PROTEIN; BETA CATENIN; F BOX PROTEIN; FES1 PROTEIN; HECT E3 UBIQUITIN LIGASE; KARYOPHERIN ALPHA; KARYOPHERIN BETA; MICROTUBULE ASSOCIATED KINENSIN MOTOR DOMAIN PROTEIN; MICROTUBULE ASSOCIATED PROTEIN; PEPTIDES AND PROTEINS; PLAKOPHILIN; U BOX E3 UBIQUITIN LIGASE; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ABIOTIC STRESS; AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BRASSICA; CHROMOSOMAL LOCALIZATION; CHROMOSOME MAP; CHROMOSOME NUMBER; CLUSTER ANALYSIS; COLD STRESS; COMPARATIVE STUDY; CONTROLLED STUDY; DEVELOPMENTAL STAGE; DOWN REGULATION; DROUGHT STRESS; DUPLICATE GENE; EUDICOT; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC LINE; MICROARRAY ANALYSIS; MONOCOT; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT DEVELOPMENT; PLANT GROWTH; PLANT PHYSIOLOGY; PROMOTER REGION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PURIFYING SELECTION; REAL TIME POLYMERASE CHAIN REACTION; RICE; SALT STRESS; SEED DEVELOPMENT; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; TANDEM REPEAT; UBIQUITINATION; UPREGULATION; VEGETATIVE STAGE; BIOLOGY; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR EVOLUTION; PHYSIOLOGICAL STRESS; PLANT CHROMOSOME; PLANT GENOME;

ARMADILLO DOMAIN PROTEINS; CHROMOSOMES, PLANT; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENOME, PLANT; MICROARRAY ANALYSIS; MULTIGENE FAMILY; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; PROMOTER REGIONS, GENETIC; STRESS, PHYSIOLOGICAL;

EID: 84900999521     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst056     Document Type: Article

References (59)

1. Andrade, M.A., Perez-Iratxeta, C. and Ponting, C.P. 2001, Protein repeats: structures, functions, and evolution, J. Struct. Biol., 1342, 117-31.
2. Akiyama, T. 2000, Wnt/beta-catenin signaling, Cytokine Growth Factor Rev., 11, 273-82.
3. Aravind, L. and Koonin, E.V. 2000, The U box is a modified RING finger - a common domain in ubiquitination, Curr. Biol., 10, 132-4.
4. Conacci-Sorrell, M., Zhurinsky, J. and Ben-Ze'ev, A. 2002, The cadherin-catenin adhesion system in signaling and cancer, J. Clin. Invest., 109, 987-91. (Pubitemid 34408571)
5. Amador, V., Monte, E., Garcia-Martinez, J.L. and Prat, S. 2001, Gibberellins signal nuclear import of PHOR1, a photoperiod-responsive protein with homology to Drosophila armadillo, Cell, 106, 343-54. (Pubitemid 32772618)
6. Kim, M., Cho, H.S., Kim, D.M., Lee, J.H. and Pai, H.S. 2003, CHRK1, a chitinase-related receptor-like kinase, interacts with NtPUB4, an armadillo repeat protein, in tobacco, Biochim. Biophys. Acta, 16,51, 50-9. (Pubitemid 38234552)
7. Kim, S., Choi, H.I., Ryu, H.J., Park, J.H., Kim, M.D. and Kim, S.Y. 2004, ARIA, an Arabidopsis arm repeat protein interacting with a transcriptional regulator of abscisic acid-responsive gene expression, is a novel abscisic acid signaling component, Plant Physiol., 136, 3639-48. (Pubitemid 41075802)
8. Zeng, L.R., Qu, S., Bordeos, A., et al. 2004, Spotted leaf11, a negative regulator of plant celldeathand defense, encodes a U-box/armadillo repeat protein endowed with E3 ubiquitin ligase activity, Plant Cell, 16, 2795-808. (Pubitemid 41071363)
9. Logan, C.Y. and Nusse, R. 2004, The Wnt signaling pathway in development and disease, Annu. Rev. Cell Dev. Biol., 20, 781-810. (Pubitemid 39488658)
10. Nelson, W.J. and Nusse, R. 2004, Convergence of Wnt, beta-catenin, and cadherin pathways, Science, 303, 1483-7. (Pubitemid 38314410)
11. Groves, M.R. and Barford, D. 1999, Topological characteristics of helical repeat proteins, Curr. Opin. Struct. Biol., 9, 83-389.
12. Coates, J.C. 2003, Armadillo repeat proteins: beyond the animal kingdom, Trends Cell Biol., 13, 463-71. (Pubitemid 37289396)
13. Bergler, J. and Hoth, S. 2011, Plant U-box armadillo repeat proteins AtPUB18 and AtPUB19 are involved in salt inhibition of germination in Arabidopsis, Plant Biol. Stuttg., 13, 725-30.
14. Mudgil, Y., Shiu, S.H., Stone, S.L., Salt, J.N. and Goring, D.R. 2004, A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family, Plant Physiol., 134, 59-66. (Pubitemid 38178680)
15. Stone, S.L., Anderson, E.M., Mullen, R.T. and Goring, D.R. 2003, ARC1 is an E3 ubiquitin ligase and promotes the ubiquitination of proteins during the rejection of self-incompatible Brassica pollen, Plant Cell, 15, 885-98. (Pubitemid 36453287)
16. Samuel, M.A., Salt, J.N., Shiu, S.H. and Goring, D.R. 2006, Multifunctional arm repeat domains in plants, Int Rev Cytol., 253, 1-26. (Pubitemid 46107113)
17. Coates, J.C. 2008, Armadillo repeat proteins: versatile regulators of plant development and signaling, Plant Cell, 10, 299-314.
18. Wang, H., Lu, Y., Jiang, T.,Berg, H., Li, C.andXia, Y.2013,The Arabidopsis U-box/ARM repeat E3 ligase AtPUB4 influences growth and degeneration of tapetal cells, and its mutation leads to conditional male sterility, Plant J., 74, 511-23.
19. Soding, J., Biegert, A. and Lupas, A.N. 2005, The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res., 33 Web Server issue, W244-8.
20. Eddy, S.R. 1998, Profile hidden Markovmodels, Bioinformatics, 14, 755-63.
21. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 28, 2731-9.
22. Comeron, J.M. 1999, K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals, Bioinformatics, 15, 763-4. (Pubitemid 29484339)
23. Blanc, G. and Wolfe, K.H. 2004, Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes, Plant Cell, 16, 1667-78. (Pubitemid 38908767)
24. Yu, J., Wang, J., Lin,W., et al. 2005, The genomes of Oryza sativa: a history of duplications, PLoS Biol., 3, e38.
25. Ray, S.,Agarwal,P., Arora, R.,Kapoor, S. andTyagi,A.K.2007, Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice Oryza sativa L. ssp. indica, Mol. Genet. Genomics, 278, 493-505. (Pubitemid 47568702)
26. Lescot, M., Dehais, P., Thijs, G., et al. 2002, PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promotersequences, Nucleic Acids Res., 30, 325-7. (Pubitemid 34685468)
27. Tewari, R., Bailes, E., Bunting, K.A. and Coates, J.C. 2010, Armadillo-repeat protein functions: questions for little creatures, Trends Cell Biol., 20, 470-81.
28. Kobe, B. and Kajava, A.V. 2000, When protein folding is simplified to protein coiling: the continuum of solenoid protein structures, Trends Biochem. Sci., 25, 509-15.
29. Fawcett, J.A., Maere, S. and Van de Peer, Y. 2009, Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event, Proc. Natl Acad. Sci. USA, 106, 5737-42.
30. Koch, M.A., Haubold, B. and Mitchell-Olds, T. 2000, Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera Brassicaceae, Mol. Biol. Evol., 17, 1483-98.
31. Blanc, G.,Hokamp,K. andWolfe, K.H. 2003,A recentpolyploidy superimposed on older large-scale duplications in the Arabidopsis genome, Genome Res., 13, 137-44.
32. Wang, X., Shi, X., Hao, B., Ge, S. and Luo, J. 2005, Duplication and DNA segmental loss in the rice genome: implications for diploidization, New Phytol., 165, 937-46. (Pubitemid 40284854)
33. Singh, A., Giri, J., Kapoor, S., Tyagi, A.K. and Pandey, G.K. 2010, Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis underabiotic stress conditionsandreproductivedevelopment, BMC Genomics, 11, 435.
34. Vij, S., Giri, J.,Dansana, P.K.,Kapoor, S.andTyagi,A.K.2008, The receptor-like cytoplasmic kinase OsRLCK, gene family in rice: organization, phylogenetic relationship, and expression during development and stress, Mol Plant., 1, 732-50.
35. Chen, W., Provart, N.J., Glazebrook, J., et al. 2002, Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses, Plant Cell, 1, 559-74. (Pubitemid 34305625)
36. Yamaguchi-Shinozaki, K. and Shinozaki, K. 2005, Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters, Trends Plant Sci., 10, 88-94. (Pubitemid 40234484)
37. Moody, L.A., Saidi, Y., Smiles, E.J., Bradshaw, S.J., Meddings, M., Winn, P.J. and Coates, J.C. 2012, ARABIDILLO gene homologues in basal land plants: species-specific gene duplication and likely functional redundancy, Planta, 236, 1927-41.
38. Nibau, C., Gibbs, D.J., Bunting, K.A., et al. 2011, ARABIDILLO proteins have a novel and conserved domain structure important for the regulation of their stability, Plant Mol. Biol., 75, 77-92.
39. Coates, J.C., Laplaze, L. and Haseloff, J. 2006, Armadillorelated proteins promote lateral root development in Arabidopsis, Proc. Natl Acad. Sci. USA, 103, 1621-6. (Pubitemid 43191214)
40. Yang, C.W., Gonzalez-Lamothe, R., Ewan, R.A., et al. 2006, The E3 ubiquitin ligase activity of arabidopsis PLANT UBOX17 and its functional tobacco homolog ACRE276 are required for cell death and defense, Plant Cell, 18, 1084-98. (Pubitemid 43956155)
41. Li, W., Dai, L. and Wang, G.L. 2012, PUB13, a U-box/ARM E3 ligase, regulates plant defense, cell death, and flowering time, Plant Signal. Behav., 7, 898-900.
42. Acosta, M.G., Ahumada, M.Á., Lassaga, S.L. and Casco, V.H. 2012, PUB16 gene expression under abiotic stress and their putative role as an ARM repeat protein in Arabidopsis thaliana self-pollination pathway, Adv. Biosci. Biotechnol., 3, 609-19.
43. Liu, J., Li, W., Ning, Y., et al. 2012, The U-Box E3 ligase SPL11/PUB13 is a convergence point of defense and flowering signaling in plants, Plant Physiol., 160, 28-37.
44. Seo, D.H., Ryu, M.Y., Jammes, F., et al. 2012, Roles of four Arabidopsis U-box E3 ubiquitin ligases in negative regulation of abscisic acid-mediated drought stress responses, Plant Physiol., 160, 556-68.
45. Drechsel,G., Bergler, J.,Wippel, K., Sauer, N., Vogelmann, K. and Hoth, S. 2011, C-terminal armadillo repeats are essential and sufficient for association of the plant U-box armadillo E3 ubiquitin ligase SAUL1 with the plasma membrane, J. Exp. Bot., 62, 775-85.
46. Cho, S.K., Ryu, M.Y., Song, C., Kwak, J.M. and Kim, W.T. 2008, Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress, Plant Cell, 20, 1899-914. (Pubitemid 352844540)
47. Trujillo, M., Ichimura, K., Casais, C. and Shirasu, K. 2008, Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis, Curr. Biol., 18, 1396-401.
48. Samuel, M.A., Mudgil, Y., Salt, J.N., Delmas, F., Ramachandran, S., Chilelli, A. and Goring, D.R. 2008, Interactions between the S-domain receptor kinases and AtPUB-ARM E3 ubiquitin ligases suggest a conserved signaling pathway in Arabidopsis, Plant Physiol., 47, 2084-95. (Pubitemid 352844247)
49. Mei, Y., Gao, H.B., Yuan, M. and Xue, H.W. 2012, The Arabidopsis ARCP protein, CSI1, which is required for microtubule stability, is necessary for root and anther development, Plant Cell, 24, 1066-80.
50. Li, S., Lei, L.,Somerville, C.R. and Gu, Y.2011,Cellulose synthase interactive protein 1 CSI1, links microtubules and cellulose synthase complexes, Proc. Natl Acad. Sci. USA, 109, 185-90.
51. Goldfarb, D.S., Corbett, A.H.,Mason, D.A., Harreman, M.T. and Adam, S.A. 2004, Importin alpha: a multipurpose nuclear-transport receptor, Trends Cell Biol., 14, 505-14. (Pubitemid 39209358)
52. Narusaka, Y., Nakashima, K., Shinwari, Z.K., et al. 2003, Interaction between two cis-acting elements, ABRE and DRE, in ABA dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses, Plant J., 34, 137-48. (Pubitemid 36536677)
53. Jiang, C., Iu, B.andSingh, J.1996,RequirementofaCCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus, Plant Mol. Biol., 30, 679-84. (Pubitemid 3040090)
54. Takaiwa, F., Oono, K. and Kato, A. 1991, Analysis of the 50 flanking region responsible for the endosperm-specific expression of a rice glutelin chimeric gene in transgenic tobacco, Plant Mol. Biol., 16, 49-58.
55. Singh, A., Baranwal, V., Shankar, A., et al. 2012, Rice phospholipase A superfamily: organization, phylogenetic and expression analysis during abiotic stresses and development, PLoS One, 7, e30947.
56. Singh, A., Kanwar, P., Pandey, A., Tyagi, A.K., Sopory, S.K., Kapoor, S. and Pandey, G.K. 2013, Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice, PLoS One, 8, e62494.
57. Lynch, M. and Conery, J.S. 2000, The evolutionary fate and consequences of duplicate genes, Science, 290, 1151-5.
58. Prince,V.E.andPickett, F.B. 2002,Splittingpairs: the diverging fates of duplicated genes, Nat. Rev. Genet., 3, 827-37. (Pubitemid 35303515)
59. Gu, Z., Nicolae, D., Lu, H.H. and Li,W.H. 2002, Rapid divergence in expression between duplicate genes inferred from microarray data, Trends Genet., 18, 609-13. (Pubitemid 35346678)