植物学报 ›› 2014, Vol. 49 ›› Issue (1): 49-62.doi: 10.3724/SP.J.1259.2014.00049

• 研究报告 • 上一篇    下一篇

水稻AT-hook基因家族生物信息学分析

张贵慰1†, 曾珏1†, 郭维1, 罗琼2*   

  1. 1云南农业大学农学与生物技术学院, 昆明 650201;
    2云南农业大学植物保护学院, 昆明 650201
  • 收稿日期:2013-03-11 修回日期:2013-06-01 出版日期:2014-01-01 发布日期:2014-01-01
  • 通讯作者: 罗琼 E-mail:qiongbf@aliyun.com
  • 基金资助:

    国家自然科学基金

Bioinformatics Analysis of the AT-hook Gene Family in Rice

Guiwei Zhang1†, Jue Zeng1†, Wei Guo1, Qiong Luo2*   

  1. 1College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China

    2College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
  • Received:2013-03-11 Revised:2013-06-01 Online:2014-01-01 Published:2014-01-01
  • Contact: Qiong Luo E-mail:qiongbf@aliyun.com

摘要: AT-hook是一种小型的DNA结合蛋白基序, 在哺乳动物非组蛋白染色体的高移动组蛋白(HMG-I/Y)中首次发现。对其它生物的研究表明, AT-hook蛋白在染色质结构组装、靶细胞特异性结合、转录调控和生长发育的调控中发挥重要作用。利用生物信息学方法, 从水稻(Oryza sativa)基因组中鉴定出了45个编码AT-hook蛋白的基因, 并对这些基因的系统进化、染色体定位及其编码蛋白的结构和功能等进行了系统的生物信息学分析。结果表明, 水稻AT-hook蛋白的结构和特性分化不显著; 45个水稻AT-hook基因可划分成5个亚族; 染色体复制是基因家族成员扩增的进化途径之一。基因数字表达分析结果显示, AT-hook基因主要在水稻幼穗中表达, 并通过qRT-PCR验证了部分基因的数字表达结果。

Abstract: The AT-hook is a small motif in DNA-binding protein that was first described in the high-mobility-group non-histone chromosomal protein HMG-I/Y. AT-hook family proteins play an important role in chromatin structure assembly, specific binding to target cells, transcription regulation and development regulation in other organisms. We identified 45 AT-hook genes from the rice genome by bioinformatics, analyzed the gene structure and chromosomal distribution, and examined the phylogenetic relationships among rice AT-hook proteins, finally constructing an unrooted tree from alignment of their full-length protein sequences in rice and Arabidopsis. AT-hook proteins grouped into 5 distinct clades (A–E), with no differences in structure or characteristics. The family members were recruited by chromosome replication. Digital gene expression analysis revealed that AT-hook genes mainly express in young panicles. We verified some of the gene expression by qRT-PCR.

中图分类号: 

  • Q786

参考文献
郭安源, 朱其慧, 陈新, 罗静初 (2007). GSDS: 基因结构显示系统. 遗传 29, 1023-1026.

唐雄杰, 郭维, 王云月, 刘林, 李成云, 罗琼 (2011). 水稻内稃发育相关基因PAL1时空表达研究. 云南农业大学学报 26, 149-155.

肖朝文, 傅永福 (2009). AT-Hook蛋白的研究进展. 中国农业科技导报 11, 12-16.

Aravind L, Landsman David (1998). AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res 26, 4413-4421.

Ashar H R, Fejzo M S, Tkachenko A (1995). Disruption of the architectural factor HMGI-C:DNA-binding AT hook motifs fused in lipemas to distinct transcriptional regulatory domains. Cell 82, 57-65.

Adams, Keith L, Wendel, Jonathan F. (2005). Polyploidy and genome evolution in plants. Curr opin plant boil 8, 135-141.

Churchill M E,Travers A (1991). A protein motifs that recognize structural features of DNA. Trends Biochem. Sci 16, 92-97.

Cardon, Guillermo, H?hmann, Susanne, Klein, Joachim, Nettesheim, Klaus, Saedler, Heinz, Huijser, Peter (1999). Molecular characterisation of the Arabidopsis SBP-box genes. Gene 237, 91-104.

Do H J, Song H, Yang H M, Kim D K, Kim N H, Kim J H, Cha K Y, Chung H M (2006). Identification of multiple nuclear localization signals in murine Elf3, an ETS transcription factor. FAS Lett 580, 1865-1871.

Delaney S K, Orford S J, Martin-Harris M, Timmis JN (2007). The fiber specificity of the cotton FSltp4 gene promoter is regulated by an AT-rich promoter region and the AT-hook transcription factor GhAT1. Plant Cell Physiol 48, 1426-1437.

Eckner R, Bimstiel M L (1989). Cloning of cDNAs coding for human HMG I and HMG Y proteins:both are capable of binding to the octamer sequence motif. Nucleic Acids Res 17, 5947-5959.

Eddy Sean R. (1998). Profile hidden Markov models. Bioinformatics 14, 755-763.

Fujimoto S, Matsunaga S, Yonemura M, Uchiyama S, Azuma T, Fukui K (2004). Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol Biol 56, 225–239.
Falvo J V, Thanos D, Maniatis T (1995). Reversal of intrinsic DNA bends in the IFN2 gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell 83, 1101-1111.

Fedele, Monica, Battista, Sabrina, Manfioletti, Guidalberto, Croce, Carlo Maria, Giancotti, Vincenzo, Fusco, Alfredo (2001). Role of the high mobility group A proteins in human lipomas. Carcinogenesis 22, 1583-1591.

Fedele M, Pierantoni G M, Berlingieri M T (2001). Overex-pression of proteins HMGA1 induces cell cycle deregulation and apeptesis in normal rat thyroid cells. Cancer Res. 61, 4583-4590.

Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006). Pfam: clans, web tools and services. Nucleic Acids Res 34, D247-251.

Gallavotti A, Malcomber S, Gaines C, Stanfield S, Whipple C, Kellogg E,and Schmidt RJ (2011). BARREN STALK FASTIGIATE1 is an AT-Hook Protein Required for the Formation of Maize Ears. Plant Cell 23, 1756-1771.

Girard F, Bello B, Laemmli UK, Gehring WJ (1998). In vivo analysis of scaffold-associated regions in Drosophila: a synthetic high-affinity SAR binding protein suppresses position effect variegation. EMBO J. 17, 2079-2085.

Jacobsen K, Laumen NB, Jansen EO, Marcker A, Poulsen C, Marcker KA(1990). HMG I-like proteins from leaf and nodule nuclei interact with different AT motifs in soybean nedulin promoters. Plant Cell 2, 85-94.

Jin Y, Lou Q, Tong H, Wang A, Cheng Z, Tang J, Li D, Zhao X, Li X, Wan J, Jiao Y, Chu C, Zhu L (2011). An AT-hook gene is required for palea formation and floral organ number control in rice. Dev Biol. 359, 277-288.

Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA, Mcwilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.

Lim PO, Kim Y, Breeze E, Koo JC, Woo HR, Jong Sang Ryu JS, Park DH, Beynon J, Tabrett A, Wollaston VB, Nam HG (2007). Overexpression of a chromatin architecture-controlling AT-hook protein extends leaf longevity and increases the post-harvest storage life of plants. Plant J. 52, 1140-1153.

Luo Q, Zhou K, Zhao X, Zeng Q, Xia H, Zhai W, Xu J, Wu X, Yang H, Zhu L (2005). Identification and fine mapping of a mutant gene for palealess spikelet in rice. Planta 221, 222-230.

Morisawa G, Han-Yama A, Moda I, Tamai A, Iwabuchi M, and Meshi T (2000). AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell 12, 1903–1916.

Metcalf CE, Wassarman DA (2006). DNA binding properties of TAF1 isoforms with two AT-hooks. J Biol chem 281, 30015-30023.

Matsushita, Akane, Furumoto, Tsuyoshi, Ishida, Sarahmi, Takahashi, Yohsuke (2007). AGF1, an AT-hook protein, is necessary for the negative feedback of AtGA3ox1 encoding GA 3-oxidase. Plant physiology 143, 1152-1162.

Martínez‐García, Jaime F, Quail, Peter H (2002). The HMG‐I/Y protein PF1 stimulates binding of the transcriptional activator GT‐2 to the PHYA gene promoter. Plant J 18, 173-183.

Ng KH, Yu H, Ito T (2009). AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation. PLoS Biol. 7, e1000251.

Onate SA, Prendergast P, Wagner JP, Nissen M, Reeves R, Pettijohn DE, Edwards DP (1994). The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences. Mol Cell Biol 14, 3376-3391.

Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007). The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 35, D883-D887.

Street IH, Shah PK, Smith AM, Avery N, Neff MM (2008). The AT-hook-containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis. Plant J 54, 1–14.

Tkachuk DC, Kohler S, Cleary ML (1992). Involvement of a homolog of Drosophila trithorax by 11q23 chromosomal translocations in acute leukemias. Cell 71, 691-700.

Vom Endt, Débora, e Silva, Marina Soares, Kijne, Jan W, Pasquali, Giancarlo, Memelink, Johan (2007). Identification of a bipartite jasmonate-responsive promoter element in the Catharanthus roseus ORCA3 transcription factor gene that interacts specifically with AT-Hook DNA-binding proteins. Plant physiology 144, 1680-1689.

Webster CI, Packman LC, Gray JC (2001). HMG-1 enhances HMG-1/Y binding to an A/T-rich enhancer element from the pea plastocyanin gene. Eur J Biochem 268, 3154-3162.

Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR (2003). The TIGR rice genome annotation resource: annotating the rice genome and cre-ating resources for plant biologis. Nucleic Acids Res. 31, 229-233.
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