Exploring the evolutionary differences of SBP-box genes targeted by miR156 and miR529 in plants

Genetica

Volumn 140, Issue 7-9, 2012, Pages 317-324

  Ling, Li Zhen ^a,b,c   Zhang, Shu Dong ^a,b  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b Plant Germplasm and Genomics Center   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Combinatorial control; Evolutionary rate; miRNA; SBP box genes

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR;

ARTICLE; GENE EXPRESSION REGULATION; GENETICS; MAIZE; MOLECULAR EVOLUTION; PHYLOGENY; PLANT; PLANT GENE; RICE;

EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MICRORNAS; ORYZA SATIVA; PHYLOGENY; PLANTS; TRANSCRIPTION FACTORS; ZEA MAYS;

BRYOPHYTA; ZEA MAYS;

EID: 84869489011     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-012-9684-3     Document Type: Article

References (34)

1. Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18(10): 758-762. doi: 10. 1016/j. cub. 2008. 04. 042.
2. Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23(9): 1751-1761. doi: 10. 1093/molbev/msl040.
3. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38(2): 228-233. doi: 10. 1038/ng1725.
4. Cheng C, Bhardwaj N, Gerstein M (2009) The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics 10: 431. doi: 10. 1186/1471-2164-10-431.
5. Chuck G, Cigan AM, Saeteurn K, Hake S (2007) The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat Genet 39(4): 544-549. doi: 10. 1038/ng2001.
6. Chuck G, Whipple C, Jackson D, Hake S (2010) The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development 137(8): 1243-1250. doi: 10. 1242/dev. 048348.
7. Cuperus JT, Fahlgren N, Carrington JC (2011) Evolution and functional diversification of MIRNA genes. Plant Cell 23(2): 431-442. doi: 10. 1105/tpc. 110. 082784.
8. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39 (Web Server issue): W155-W159. doi: 10. 1093/nar/gkr319.
9. German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26(8): 941-946. doi: 10. 1038/nbt1417.
10. Guo AY, Zhu QH, Gu X, Ge S, Yang J, Luo J (2008) Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene 418(1-2): 1-8. doi: 10. 1016/j. gene. 2008. 03. 016.
11. Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC, Green PJ (2011) Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 23(12): 4185-4207. doi: 10. 1105/tpc. 111. 089045.
12. Jiang C, Gu X, Peterson T (2004) Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica. Genome Biol 5(7): R46. doi: 10. 1186/gb-2004-5-7-r46.
13. Kong H, Leebens-Mack J, Ni W, dePamphilis CW, Ma H (2004) Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications. Mol Biol Evol 21(1): 117-128. doi: 10. 1093/molbev/msh001.
14. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39 (Database issue): D152-D157. doi: 10. 1093/nar/gkq1027.
15. Lawrence CJ, Malmberg RL, Muszynski MG, Dawe RK (2002) Maximum likelihood methods reveal conservation of function among closely related kinesin families. J Mol Evol 54(1): 42-53. doi: 10. 1007/s00239-001-0016-y.
16. Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R (2010) Transcriptome-wide identification of microRNA targets in rice. Plant J 62(5): 742-759. doi: 10. 1111/j. 1365-313X. 2010. 04187. x.
17. Ling LZ, Zhang SD (2012) Unraveling the distribution and evolution of miR156-targeted SPLs in plants by phylogenetic analysis. Plant Divers Resour 34(1): 33-46.
18. Maher C, Stein L, Ware D (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res 16(4): 510-519. doi: 10. 1101/gr. 4680506.
19. Patthy L (1999) Genome evolution and the evolution of exon-shuffling-a review. Gene 238(1): 103-114.
20. Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38(Suppl): S8-S13. doi: 10. 1038/ng1798.
21. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110(4): 513-520.
22. Riano-Pachon DM, Ruzicic S, Dreyer I, Mueller-Roeber B (2007) PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8: 42. doi: 10. 1186/1471-2105-8-42.
23. Roy SW (2003) Recent evidence for the exon theory of genes. Genetica 118(2-3): 251-266.
24. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8(4): 517-527. doi: 10. 1016/j. devcel. 2005. 01. 018.
25. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10): 2731-2739. doi: 10. 1093/molbev/msr121.
26. 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(24): 4876-4882.
27. Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15(8): 1749-1770.
28. Toth-Petroczy A, Tawfik DS (2011) Slow protein evolutionary rates are dictated by surface-core association. Proc Natl Acad Sci U S A 108(27): 11151-11156. doi: 10. 1073/pnas. 1015994108.
29. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136(4): 669-687. doi: 10. 1016/j. cell. 2009. 01. 046.
30. Wang S, Zhu QH, Guo X, Gui Y, Bao J, Helliwell C, Fan L (2007) Molecular evolution and selection of a gene encoding two tandem microRNAs in rice. FEBS Lett 581(24): 4789-4793. doi: 10. 1016/j. febslet. 2007. 09. 002.
31. Wu G, Poethig RS (2006) Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133(18): 3539-3547. doi: 10. 1242/dev. 02521.
32. Xie K, Wu C, Xiong L (2006) Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol 142(1): 280-293. doi: 10. 1104/pp. 106. 084475.
33. Xing S, Salinas M, Hohmann S, Berndtgen R, Huijser P (2010) miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis. Plant Cell 22(12): 3935-3950. doi: 10. 1105/tpc. 110. 079343.
34. Zheng Y, Li YF, Sunkar R, Zhang W (2011) SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants. Nucleic Acids Res. doi: 10. 1093/nar/gkr1092.