miR156靶基因SPL在植物中的系统分布和进化模式分析

doi:10.3724/SP.J.1143.2012.11117

摘要/Abstract

摘要：

Squamosa promoterbinding proteinlike genes (SPLs)在植物发育过程中具有重要作用。很多SPLs被miR156调节，然而，对于它们在植物中的系统分布和进化模式还知之甚少。本文对9个测序物种（藻类，苔藓，石松，单子叶和双子叶植物）的183个SPLs进行了生物信息学分析。结果表明miR156应答元件（MREs）仅在陆生植物SPLs中发现，藻类中不存在。系统进化分析显示陆生植物SPLs分为两大分支：group I和group II。 MiR156靶基因仅分布于group II，表明它们有着共同的祖先。Group II进一步分为7个亚支(IIaIIg)，miR156靶基因分布在除IId外的其余6个亚支的特定SPLs。系统分类与基因结构的相关性反映了SPL靶基因结构上的变化。在进化过程中，它们可能发生外显子的丢失且伴随MRE的丢失。另外，基因重复对SPL靶基因的丰度变化影响很大，尤其是被子植物与低等植物分歧后它们数量明显增加。以拟南芥为模式植物分析发现串联重复和片段重复是SPL靶基因扩张的主要机制。

关键词: 系统分析, 基因重复, 基因结构, microRNA, 转录因子

Abstract:

Squamosa promoterbinding proteinlike genes (SPLs) are critical during plant development and mostly regulated by miR156. However, little is known about phylogenetic distribution and evolutionary patterns of miR156targeted SPLs. In this study, 183 SPLs from nine genomesequenced species representing algae, bryophytes, lycophyte, monocots, and eudicots were computationally analyzed. Our results showed that miR156 responsive elements (MREs) on SPLs were present in land plants but absent from unicellular green algae. Phylogenetic analysis revealed that miR156targeted SPLs only distributed in group II not group I of land plants, suggesting they originated from a common ancestor. In addition, group II were further divided into seven subgroups (IIaIIg) and miR156targeted SPLs distributed in some specific members of SPLs from six subgroups except subgroup IId. Such distribution pattern was well elucidated by gene structure evolution of miR156targeted SPLs based on the correlation of phylogenetic classification and gene structure. They could suffer from the exon loss events combined with MREs loss during evolution. Moreover, gene duplication contributed to the abundance of miR156targeted SPLs, which had significantly increased after angiosperms and lower plants split. With Arabidopsis as the model species, we found segmental and tandem gene duplications predominated during miR156targeted SPLs expansion. Taken together, these results provide better insights in understanding the function diversity and evolution of miR156targeted SPLs in plants.

Key words: Phylogenetic analysis, Gene duplication, Gene structure, MicroRNA

中图分类号:

Q 78

凌立贞1、2, 张书东1. miR156靶基因SPL在植物中的系统分布和进化模式分析[J]. Plant Diversity, 2012, 34(01): 33-46.

LING Li-Zhen-, ZHANG Shu-Dong. Unraveling the Distribution and Evolution of miR156targeted SPLs in Plants by Phylogenetic Analysis[J]. Plant Diversity, 2012, 34(01): 33-46.

参考文献

Arazi T, TalmorNeiman M, Stav R et al., 2005. Cloning and characterization of microRNAs from moss［J］. The Plant Journal, 43: 837—848
Birkenbihl RP, Jach G, Saedler H et al., 2005. Functional dissection of the plantspecific SBPdomain: overlap of the DNAbinding and nuclear localization domains［J］. Journal of Molecular Biology, 352: 585—596
Blanc G, Hokamp K, Wolfe KH, 2003. A recent polyploidy superimposed on older largescale duplications in the Arabidopsis genome［J］. Genome Research, 13: 137—144
Bowers JE, Chapman BA, Rong J et al., 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events［J］. Nature, 422: 433—438
Cardon GH, Hohmann S, Nettesheim K et al., 1997. Functional analysis of the Arabidopsis thaliana SBPbox gene SPL3: a novel gene involved in the floral transition［J］. The Plant Journal, 12: 367—377
Chen X, Zhang Z, Liu D et al., 2010. SQUAMOSA promoterbinding proteinlike transcription factors: star players for plant growth and development［J］. Journal of Integrative Plant Biology, 52: 946—951
Chuck G, Cigan AM, Saeteurn K et al., 2007. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA［J］. Nature Genetics, 39: 544—549
Derr LK, 1998. The involvement of cellular recombination and repair genes in RNAmediated recombination in Saccharomyces cerevisiae［J］. Genetics, 148: 937—945
Fornara F, Coupland G, 2009. Plant phase transitions make a SPLash［J］. Cell, 138: 625—627
Gandikota M, Birkenbihl RP, Hohmann S et al., 2007. The miRNA156/157 recognition element in the 3’ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings［J］. The Plant Journal, 49: 683—693
Guo AY, Zhu QH, Gu X et al., 2008. Genomewide identification and evolutionary analysis of the plant specific SBPbox transcription factor family［J］. Gene, 418: 1—8
He K, Guo AY, Gao G et al., 2010. Computational identification of plant transcription factors and the construction of the PlantTFDB database［J］. Methods in Molecular Biology, 674: 351—368
Jiao Y, Wang Y, Xue D et al., 2010. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice［J］. Nature Genetics, 42: 541—544
Kim S, Soltis PS, Wall K et al., 2006. Phylogeny and domain evolution in the APETALA2like gene family［J］. Molecular Biology and Evolution, 23: 107—120
Kozomara A, GriffithsJones S, 2011. miRBase: integrating microRNA annotation and deepsequencing data［J］. Nucleic Acids Research, 39: D157
Kropat J, Tottey S, Birkenbihl RP et al., 2005. A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element［J］. Proceedings of the National Academy of Sciences of the United States of America, 102: 18730—18735
Li YF, Zheng Y, AddoQuaye C et al., 2010. Transcriptomewide identification of microRNA targets in rice［J］. The Plant Journal, 62: 742—759
Manning K, Tor M, Poole M et al., 2006. A naturally occurring epigenetic mutation in a gene encoding an SBPbox transcription factor inhibits tomato fruit ripening［J］. Nature Genetics, 38: 948—952
Martin RC, Liu PP, Goloviznina NA et al., 2010. microRNA, seeds, and Darwin?: diverse function of miRNA in seed biology and plant responses to stress［J］. Journal of Experimental Botany, 61: 2229—2234
Miura K, Ikeda M, Matsubara A et al., 2010. OsSPL14 promotes panicle branching and higher grain productivity in rice［J］. Nature Genetics, 42: 545—549
Molnar A, Schwach F, Studholme DJ et al., 2007. miRNAs control gene expression in the singlecell alga Chlamydomonas reinhardtii［J］. Nature, 447: 1129
Moreno MA, Harper LC, Krueger RW et al., 1997. Liguleless1 encodes a nuclearlocalized protein required for induction of ligules and auricles during maize leaf organogenesis［J］. Genes & Development, 11: 616—628
Mourier T, Jeffares DC, 2003. Eukaryotic intron loss［J］. Science, 300: 1393
Nonogaki H, 2010. microRNA gene regulation cascades during early stages of plant development［J］. Plant and Cell Physiology, 51: 1840—1846
PerezRodriguez P, RianoPachon DM, Correa LG et al., 2009. PlnTFDB: updated content and new features of the plant transcription factor database［J］. Nucleic Acids Research, 38: D822—D827
Poethig RS, 2010. The past, present, and future of vegetative phase change［J］. Plant Physiol, 154: 541—544
RianoPachon DM, Ruzicic S, Dreyer I et al., 2007. PlnTFDB: an integrative plant transcription factor database［J］. BMC Bioinformatics, 8: 42
Riese M, Hohmann S, Saedler H et al., 2007. Comparative analysis of the SBPbox gene families in P.patens and seed plants［J］. Gene, 401: 28—37
Schwab R, Palatnik JF, Riester M et al., 2005. Specific effects of microRNAs on the plant transcriptome［J］. Developmental Cell, 8: 517—527
Schwarz S, Grande AV, Bujdoso N et al., 2008. The microRNA regulated SBPbox genes SPL9 and SPL15 control shoot maturation in Arabidopsis［J］. Plant Molecular Biology, 67: 183—195
Thompson JD, Gibson TJ, Plewniak F et al., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools［J］. Nucleic Acids Research, 25: 4876—4882
Vision TJ, Brown DG, Tanksley SD, 2000. The origins of genomic duplications in Arabidopsis［J］. Science, 290: 2114—2117
Wang D, Guo Y, Wu C et al., 2008. Genomewide analysis of CCCH zinc finger family in Arabidopsis and rice［J］. BMC Genomics, 9: 44
Wang JW, Czech B, Weigel D, 2009. miR156regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana［J］. Cell, 138: 738—749
Worden AZ, Lee JH, Mock T et al., 2009. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas［J］. Science, 324: 268—272
Wu G, Park MY, Conway SR et al., 2009. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis［J］. Cell, 138: 750—759
Wu G, Poethig RS, 2006. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3［J］. Development, 133: 3539—3547
Xie K, Wu C, Xiong L, 2006. Genomic organization, differential expression, and interaction of SQUAMOSA promoterbindinglike transcription factors and microRNA156 in rice［J］. Plant Physiology, 142: 280—293
Xing S, Salinas M, Hohmann S et al., 2010. miR156Targeted and nontargeted SBPbox transcription factors act in concert to secure male fertility in Arabidopsis［J］. The Plant Cell, 22: 3935—3950
Yamasaki H, Hayashi M, Fukazawa M et al., 2009. SQUAMOSA promoter Binding ProteinLike7 Is a central regulator for copper Homeostasis in Arabidopsis［J］. The Plant Cell, 21: 347—361
Yamasaki K, Kigawa T, Inoue M et al., 2004. A novel zincbinding motif revealed by solution structures of DNAbinding domains of Arabidopsis SBPfamily transcription factors［J］. Journal of Molecular Biology, 337: 49—63
Yang Z, Wang X, Gu S et al., 2008. Comparative study of SBPbox gene family in Arabidopsis and rice［J］. Gene, 407: 1—11
Zhang Y, 2005. miRU: an automated plant miRNA target prediction server［J］. Nucleic Acids Research, 33: W701—W704

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