Bioinformatics and Identification of eIF5A Gene Family in Phalaenopsis equestris (Schauer) Rchb. f.
-
摘要: 为了系统分析兰花真核翻译起始因子5A（Eukaryotic translation initiation factor 5A，eIF5A）基因家族在兰花中如何发挥作用，利用兰花基因组数据库，通过生物信息学的方法，鉴定兰花eIF5A基因家族的基因结构、编码蛋白和磷酸化位点预测，通过序列比对进行进化分析。结果表明，兰花eIF5A基因家族含有eIF5A1和eIF5A2两个基因，分别含有5个和6个外显子。MEME保守基序分析显示，兰花eIF5A1和eIF5A2蛋白均含有1个保守的DNA结合寡核苷酸结合结构域（PF01287）。磷酸化位点预测分析表明兰花eIF5A1和eIF5A2蛋白均含有大量的潜在磷酸化位点。以上结果将为今后揭示兰花eIF5A1和eIF5A2蛋白的功能提供重要的线索。Abstract: To understand the functions of eIF5A gene family in Phalaenopsis equestris, the genome database and bioinformatics were applied to obtain their gene structures, coded proteins, and predicted phosphorylation sites for analysis. The results showed that the eIF5A1 and eIF5A2 genes in P. equestris genome contained 5 and 6 extrons, respectively. The multiple alignments and motif displays rendered from the MEME method indicated that all PeeIF5A1 and PeeIF5A2 proteins contained one conserved DNA binding OB binding motif, PF01287. The phosphorylation site prediction on the proteins showed numerous sites.These results would provide the important clues for functional studies to reveal the role of PeeIF5A1 and PeeIF5A2 proteins in P.equestris.
-
Key words:
- Phalaenopsis equestris /
- eIF5A /
- gene family /
- phylogeny analysis
-
图 2 兰花eIF5A蛋白跨膜结构预测
Figure 2. Predicted transmembrane structure of eIF5A proteins in P. equestris
图 3 小麦、拟南芥、美洲黑杨、毛果杨和兰花的eIF5A基因家族编码蛋白保守基序分布
Figure 3. Distributions of conserved motifs of eIF5A proteins in Triticum aestivum, Arabidopsis, Populus davidiana, Populus trichocarpa and P. equestris
图 5 拟南芥、小麦、毛果杨、美洲黑杨和兰花的eIF5A蛋白进化树
注：利用MEGA6.0软件构建进化树，5种植物16个eIF5A蛋白分为3个组。
Figure 5. Phylogenetic trees of eIF5A proteins in Arabidopsis, T. aestivum, P. trichocarpa, P. davidiana and P. equestris
图 6 兰花eIF5A蛋白磷酸化位点预测
Figure 6. Predicted phosphorylation sites of eIF5A proteins in P. equestris
表 1 兰花eIF5A基因家族的基本特征
Table 1. Characteristics of PeeIF5A genes in P. equestris
基因名称 定位名称 基因长度 脚手架名称 位置 开放阅读框 蛋白 外显子个数 PeeIF5A1 PEQU_04554 13599 Scaffold000224 1858318-1871917 - 480 159 5 PeeIF5A2 PEQU_04168 16241 Scaffold000002 76637607-76653848 + 606 201 6 
下载: 导出CSV
表 2 兰花eIF5A蛋白的二级结构信息
Table 2. Information on secondary structure of eIF5A proteins in P. equestris
eIF5A家族 α-螺旋/% β-折叠/% β-转角/% 无规则卷曲/% PeeIF5A1 28.93 19.50 9.43 42.14 PeeIF5A2 24.88 24.38 10.45 40.30
下载: 导出CSV
表 3 兰花基因组中eIF5A蛋白磷酸化位点分析
Table 3. Phosphorylation sites analysis on eIF5A proteins in P. equestris
eIF5A家族 丝氨酸 苏氨酸 酪氨酸 PeeIF5A1 6 7 2 PeeIF5A2 13 7 2
下载: 导出CSV
-
[1] SHIN B S, KATOH T, GUTIERREZ E, et al. Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis[J]. Nucleic Acids Res, 2017, 45(14):8392-8402. doi: 10.1093/nar/gkx532 [2] KYRPIDES N C, WOESE C R. Universally conserved translation initiation factors[J]. Proc Natl Acad Sci USA, 1998, 95(1):224-228. doi: 10.1073/pnas.95.1.224 [3] SCHNIER J, SCHWELBERGER H G, SMIT-MCBRIDE Z, et al. Translation initiation factor 5A and its hypusine modification are essential for cell viability in the yeast Saccharomyces cerevisiae[J]. Mol Cell Biol, 1991, 11(6):3105-3114. doi: 10.1128/MCB.11.6.3105 [4] KEMPER W M, BERRY K W, MERRICK W C. Purification and properties of rabbit reticulocyte protein synthesis initiation factors M2Balpha and M2Bbeta[J]. J Biol Chem, 1976, 251(18):5551-5557. https://www.researchgate.net/publication/22190341_Purification_and_properties_of_rabbit_reticulocyte_protein_synthesis_initiation_factors_M2Ba_and_M2Bb [5] BENNE R, HERSHEY J W. The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes[J]. J Biol Chem, 1978, 253(9):3078-3087. https://www.researchgate.net/publication/22501363_Mechanism_of_action_of_protein-synthesis_initiation-factors_from_rabbit_reticulocytes [6] THOMPSON J E, HOPKINS M T, TAYLOR C, et al. Regulation of senescence by eukaryotic translation initiation factor 5A:implications for plant growth and development[J]. Trends Plant Sci, 2004, 9(4):174-179. doi: 10.1016/j.tplants.2004.02.008 [7] HOPKINS M T, LAMPI Y, WANG T W, et al. Eukaryotic translation initiation factor 5A is involved in pathogen-induced cell death and development of disease symptoms in Arabidopsis[J]. Plant Physiol, 2008, 148(1):479-489. doi: 10.1104/pp.108.118869 [8] FENG H, CHEN Q, FENG J, et al. Functional characterization of the Arabidopsis eukaryotic translation initiation factor 5A-2 that plays a crucial role in plant growth and development by regulating cell division, cell growth, and cell death[J]. Plant Physiol, 2007, 144(3):1531-1545. doi: 10.1104/pp.107.098079 [9] MA F, LIU Z, WANG T, et al. Arabidopsis eIF5A3 influences growth and the response to osmotic and nutrient stress[J]. Plant Cell Environ, 2010, 33(10):1682-1696. doi: 10.1111/pce.2010.33.issue-10 [10] CAI J, LIU X, VANNESTE K, et al. The genome sequence of the orchid Phalaenopsis equestris[J]. Nat Genet, 2014, 47(1):186-186. https://www.researchgate.net/publication/283976835_Analysis_of_the_TCP_genes_expressed_in_the_inflorescence_of_the_orchid_Orchis_italica [11] SIEVERS F, WILM A, DINEEN D, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega[J]. Mol Syst Biol, 2011, 7(1):1429-1432. http://web.engr.illinois.edu/~warnow/aayushee-clustal-omega.pdf [12] GEOURJON C, DELEAGE G. SOPMA:significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments[J]. Comput Appl Biosci, 1995, 11(6):681-684. https://www.researchgate.net/publication/14395480_SOPMA_Significant_improvements_in_protein_secondary_structure_prediction_by_consensus_prediction_from_multiple_alignments [13] 张演义, 吕福堂, 张全军, 等.葡萄MAPKK基因家族的识别与分析[J].西南农业学报, 2015, 28(4):1791-1797. http://www.chinaagrisci.com/article/2014/0578-1752-47-17-3444.html [14] BAILEY T L, BODEN M, BUSKE F A, et al. MEME SUITE:Tools for motif discovery and searching[J]. Nucleic Acids Res, 2009, 37(S2):202-208. https://www.hsls.pitt.edu/obrc/index.php?page=URL1153939718 [15] 张杰伟, 丁莉萍, 陈亚娟, 等.杨树磷酸肌醇特异性磷脂酶C基因家族鉴定与分析[J].福建农业学报, 2016, 31(11):185-190. http://www.fjnyxb.cn/CN/abstract/abstract3053.shtml [16] LARKIN M A, BLACKSHIELDS G, BROWN N P, et al. Clustal W and clustal X version 2.0[J]. Bioinformatics, 2007, 23(21):2947-2948. doi: 10.1093/bioinformatics/btm404 [17] 邵龙婷, 郑唐春, 臧丽娜, 等.毛果杨Eukaryotic translation initiation factor 5A (eIF5A)同源基因的生物信息学分析[J].安徽农业大学学报, 2014, 41(1):141-149. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=ahnydxxb201401028 [18] 周建平, 杨足君, 冯娟, 等.小麦蛋白翻译起始因子5A基因(eIF5A)的克隆与分析[J].遗传, 2006, 28(5):571-577. http://www.chinaagrisci.com/article/2014/0578-1752-47-19-3746.html [19] TAMURA K, STECHER G, PETERSON D, et al. MEGA6:Molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12):2725-2729. doi: 10.1093/molbev/mst197 [20] NAKANO T, SUZUKI K, FUJIMURA T, et al. Genome-wide analysis of the ERF gene family in Arabidopsis and rice[J]. Plant Physiol, 2006, 140(2):411-432. doi: 10.1104/pp.105.073783 [21] 管阳, 王宏芝, 张杰伟, 等.毛白杨翻译起始因子基因PtoeIF5A2的克隆及其表达特性分析[J].林业科学, 2014, 50(2):63-69. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=lykx201402010 [22] 张利姣, 张杰伟, 陈亚娟, 等.毛白杨真核细胞翻译起始因子5A基因(PtoeIF5A4)的克隆与表达分析[J].农业生物技术学报, 2013, 21(8):949-956. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=nyswjsxb201308008 [23] LEBSKA M, CIESIELSKI A, SZYMONA L, et al. Phosphorylation of maize eIF5A by CK2:identification of phosphorylated residue and influence on intracellular localization of eIF5A[J]. J Biol Chem, 2010, 285(9):6217-6226. doi: 10.1074/jbc.M109.018770 -
点击查看大图
计量
- 文章访问数: 1476
- HTML全文浏览量: 333
- PDF下载量: 108
- 被引次数: 0
