SQUAMOSA promoter binding protein-like7 regulated microRNA408 is required for vegetative development in Arabidopsis

Plant Journal

Volumn 74, Issue 1, 2013, Pages 98-109

  Zhang, Huiyong ^a   Li, Lei ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Arabidopsis; copper; development; miR408; SPL7

Indexed keywords

ARABIDOPSIS; CONSTITUTIVE EXPRESSIONS; DEVELOPMENT; ENVIRONMENTAL CONDITIONS; MIR408; SPL7; TARGET GENE EXPRESSION; VEGETATIVE DEVELOPMENT;

DEFECTS; RNA; TRANSCRIPTION FACTORS;

COPPER;

ARABIDOPSIS PROTEIN; BACTERIAL DNA; DNA BINDING PROTEIN; MICRORNA; PLANT RNA; SPL7 PROTEIN, ARABIDOPSIS; T DNA; T-DNA; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PROMOTER REGION; TRANSGENIC PLANT;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA, BACTERIAL; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; MICRORNAS; MUTAGENESIS, INSERTIONAL; PLANTS, GENETICALLY MODIFIED; PROMOTER REGIONS, GENETIC; RNA, PLANT; TRANSCRIPTION FACTORS;

ARABIDOPSIS; EMBRYOPHYTA;

EID: 84875365879     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12107     Document Type: Article

References (46)

1. Abdel-Ghany, S.E., and, Pilon, M., (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J. Biol. Chem. 283, 15932-15945.
2. Alves, L. Jr, Niemeier, S., Hauenschild, A., Rehmsmeier, M., and, Merkle, T., (2009) Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Res., 37, 4010-4021.
3. Axtell, M.J., and, Bowman, J.L., (2008) Evolution of plant microRNAs and their targets. Trends Plant Sci. 13, 343-349.
4. Bartel, D.P., (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
5. Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M., Dunoyer, P., Yamamoto, Y.Y., Sieburth, L., and, Voinnet, O., (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science, 320, 1185-1190.
6. Brunaud, V., Balzergue, S., Dubreucq, B., et al. (2002) T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep., 3, 1152-1157.
7. Burkhead, J.L., Reynolds, K.A., Abdel-Ghany, S.E., Cohu, C.M., and, Pilon, M., (2009) Copper homeostasis. New Phytol. 182, 799-816.
8. Chen, K., and, Rajewsky, N., (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat. Rev. Genet. 8, 93-103.
9. Clough, S.J., and, Bent, A.F., (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743.
10. Eamens, A.L., Agius, C., Smith, N.A., Waterhouse, P.M., and, Wang, M.B., (2011) Efficient silencing of endogenous microRNAs using artificial microRNAs in Arabidopsis thaliana. Mol. Plant, 4, 157-170.
11. Fahlgren, N., Howell, M.D., Kasschau, K.D., et al. (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE, 2, e219.
12. Festa, R.A., and, Thiele, D.J., (2011) Copper: an essential metal in biology. Curr. Biol. 21, R877-R883.
13. Garcia, P., and, Frampton, J., (2008) Hematopoietic lineage commitment: miRNAs add specificity to a widely expressed transcription factor. Dev. Cell, 14, 815-816.
14. Hobert, O., (2008) Gene regulation by transcription factors and microRNAs. Science, 319, 1785-1786.
15. Jones-Rhoades, M.W., and, Bartel, D.P., (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell, 14, 787-799.
16. Jones-Rhoades, M.W., Bartel, D.P., and, Bartel, B., (2006) MicroRNAS and their regulatory roles in plants. Annu. Rev. Plant Biol. 57, 19-53.
17. Kantar, M., Unver, T., and, Budak, H., (2010) Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Funct. Integr. Genomics, 10, 493-507.
18. Kasschau, K.D., Xie, Z., Allen, E., Llave, C., Chapman, E.J., Krizan, K.A., and, Carrington, J.C., (2003) P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev. Cell, 4, 205-217.
19. Kozomara, A., and, Griffiths-Jones, S., (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157.
20. Kropat, J., Tottey, S., Birkenbihl, R.P., Depege, N., Huijser, P., and, Merchant, S., (2005) A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element. Proc. Natl Acad. Sci. U S A, 102, 18730-18735.
21. Lee, R.C., Feinbaum, R.L., and, Ambros, V., (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
22. Li, T., Li, H., Zhang, Y.X., and, Liu, J.Y., (2010) Identification and analysis of seven HO-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acids Res. 39, 2821-2833.
23. Llave, C., Xie, Z., Kasschau, K.D., and, Carrington, J.C., (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053-2056.
24. Lu, S., Sun, Y.H., Shi, R., Clark, C., Li, L., and, Chiang, V.L., (2005) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell, 17, 2186-2203.
25. Martinez, N.J., Ow, M.C., Barrasa, M.I., Hammell, M., Sequerra, R., Doucette-Stamm, L., Roth, F.P., Ambros, V.R., and, Walhout, A.J., (2008) A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev. 22, 2535-2549.
26. Maunoury, N., and, Vaucheret, H., (2011) AGO1 and AGO2 act redundantly in miR408-mediated Plantacyanin regulation. PLoS ONE, 6, e28729.
27. Nagae, M., Nakata, M., and, Takahashi, Y., (2008) Identification of negative cis-acting elements in response to copper in the chloroplastic iron superoxide dismutase gene of the moss Barbula unguiculata. Plant Physiol. 146, 1687-1696.
28. Palmer, C.M., and, Guerinot, M.L., (2009) Facing the challenges of Cu, Fe and Zn homeostasis in plants. Nat. Chem. Biol. 5, 333-340.
29. Quinn, J.M., and, Merchant, S., (1995) Two copper-responsive elements associated with the Chlamydomonas Cyc6 gene function as targets for transcriptional activators. Plant Cell, 7, 623-628.
30. Quinn, J.M., Nakamoto, S.S., and, Merchant, S., (1999) Induction of coproporphyrinogen oxidase in Chlamydomonas chloroplasts occurs via transcriptional regulation of Cpx1 mediated by copper response elements and increased translation from a copper deficiency-specific form of the transcript. J. Biol. Chem. 274, 14444-14454.
31. Re, A., Cora, D., Taverna, D., and, Caselle, M., (2009) Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. Mol. BioSyst. 5, 854-867.
32. Ren, L., and, Tang, G., (2012) Identification of sucrose-responsive microRNAs reveals sucrose-regulated copper accumulations in an SPL7-dependent and independent manner in Arabidopsis thaliana. Plant Sci. 187, 59-68.
33. Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M., and, Weigel, D., (2005) Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 8, 517-527.
34. Schwab, R., Ossowski, S., Riester, M., Warthmann, N., and, Weigel, D., (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell, 18, 1121-1133.
35. Schwab, R., Ossowski, S., Warthmann, N., and, Weigel, D., (2010) Directed gene silencing with artificial microRNAs. Methods Mol. Biol. 592, 71-88.
36. Shalgi, R., Lieber, D., Oren, M., and, Pilpel, Y., (2007) Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol. 3, e131.
37. Sommer, F., Kropat, J., Malasarn, D., Grossoehme, N.E., Chen, X., Giedroc, D.P., and, Merchant, S.S., (2010) The CRR1 nutritional copper sensor in Chlamydomonas contains two distinct metal-responsive domains. Plant Cell, 22, 4098-4113.
38. Trindade, I., Capitao, C., Dalmay, T., Fevereiro, M.P., and, Santos, D.M., (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta, 231, 705-716.
39. Tsang, J., Zhu, J., and, van Oudenaarden, A., (2007) MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell, 26, 753-767.
40. Voinnet, O., (2009) Origin, biogenesis, and activity of plant microRNAs. Cell, 136, 669-687.
41. Wightman, B., Ha, I., and, Ruvkun, G., (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 75, 855-862.
42. Yamasaki, H., Abdel-Ghany, S.E., Cohu, C.M., Kobayashi, Y., Shikanai, T., and, Pilon, M., (2007) Regulation of copper homeostasis by micro-RNA in Arabidopsis. J. Biol. Chem. 282, 16369-16378.
43. Yamasaki, H., Hayashi, M., Fukazawa, M., Kobayashi, Y., and, Shikanai, T., (2009) SQUAMOSA promoter binding protein-like7 is a central regulator for copper homeostasis in Arabidopsis. Plant Cell, 21, 347-361.
44. Yu, X., Lin, J., Zack, D.J., Mendell, J.T., and, Qian, J., (2008) Analysis of regulatory network topology reveals functionally distinct classes of microRNAs. Nucleic Acids Res. 36, 6494-6503.
45. Zhang, B., Wang, Q., Wang, K., Pan, X., Liu, F., Guo, T., Cobb, G.P., and, Anderson, T.A., (2007) Identification of cotton microRNAs and their targets. Gene, 397, 26-37.
46. Zhang, H., He, H., Wang, X., Wang, X., Yang, X., Li, L., and, Deng, X.W., (2011) Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J. 65, 346-358.