摘要
【目的】分析‘红阳’猕猴桃全基因组AP2/EREBP转录因子家族。【方法】利用Kiwifruit Genome Database、EMBI、TAIR、SMART、Pfam、MEME、Protparam、SOPM、SWISS-MODEL、Signal P4.1 Sever网站,和Clustal X2、Bio Edit、MEGA6.0、Map Inspect、MEV软件,分析‘红阳’猕猴桃AP2/EREBP转录因子类型、结构域、系谱进化、蛋白理化性质及高级结构、信号肽分析、基因定位、序列元件和基因表达模式。【结果】‘红阳’猕猴桃全基因组中有204条AP2/EREBP转录因子,根据其结构域划分为4个亚家族。进行多序列比对和系谱进化分析,发现2个亚家族各分为6个亚组。生物信息学分析表明,204条蛋白氨基酸序列高级结构与拟南芥AP2/EREBP转录因子相似性较高。其中存在2条分泌型蛋白。基因定位表明,该家族基因在10号染色体无定位;有染色存在串联复制现象。同源拟南芥基因表达模式分析表明,AP2/EREBP转录因子对外界胁迫有显著性表达。【结论】利用生物信息学方法获得204条猕猴桃AP2/EREBP家族转录因子,并与拟南芥AP2/EREBP转录因子进行系谱进化、结构域、基因定位和同源表达等分析,结果表明猕猴桃AP2/EREBP转录因子在进化过程中比较保守,并参与了植物发育和胁迫应答调控。
[Objective] AP2/EREBP transcription factor family is a plant-specific transcription factor, which plays an important role in plant growth, development and stress response. It contains at least one AP2 binding domain and about 60-70 highly conserved amino acids. The function of the AP2/EREBP transcription factor family of the genome of Actinidia chinensis was analyzed with the completion of se- quencing of the full genome of ＇Hongyang＇ kiwifruit. [Methods ] AP2/EREBP family transcription factors were analyzed by bioinformatics. The protein and nucleic acid sequence of AP2/EREBP transcription fac- tor of kiwifruit and Arabidopsis were obtained by Kiwifruit Genome Database and TAIR database. And the domains of the AP2/EREBP transcription were analyzed by SMART, Pfam. The AP2/EREBP transcription factor was used for sequence element analysis. The domain sequence mapping was analyzed by MEME. In order to analyze the evolutionary relationship of 204 AP2/EREBP transcription factors in ＇ Hon-gyang＇ kiwifruit, ClustalX2 and MEGA6.0 were used to sequence the AP2/EREBP chinensis and Arabidopsis thaliana, and to carry out the phylogenetic analysis. The erties, secondary structure, tertiary structure, and signal peptide analysis of the AP transcripts of Actinidia Physicochemical prop- 2/EREBP transcription factor protein sequence of Actinidia chinensis were carried out using Protparam, SOPM, SWISS-MODEL and SignalP4.1 Sever. The Kiwifruit AP2/EtlEBP transcription factor sequence information was obtained from the Kiwifruit Genome Database. The MapInspect tool was used to construct the gene mapping map. The Arabidopsis thaliana AP2/EREBP transcription factor local database was constructed using BioEdit software. Blast was used to obtain the Arabidopsis thaliana sequence of AP2/EREBP transcription factor, and the Arabidopsis thaliana expression data was downloaded from EBI. The MEV tool was used to log in the downloaded data and to make an expression heat-map. [Results] The protein and nucleic acid se- quence of AP2/EREBP transcription factor of 204 kiwifruit were obtained from Kiwifruit Genome Data- base. AP2/EREBP transcription factor was divided into four subfamilies of AP2, RAV, ERF, and DREB by SMART and Pfam. In addition to the AP2 and B3 domains, the AP2/EREBP transcription factor of ki- wifruit contained ＂UQ_CON MBOAT BAG LRR Malectin RRM Mito_carr C2 Co- pine HEAT＂ and ＂Vacl4_Fabl_bd＂ domains. Sequence element analysis showed that Motifl belonged to the AP2 domain, Motif2, and Motif3 belonged to the B3 domain of RAV subfamily. Motifl, Motif2 and Motif3 belonged to the AP2 domain of AP2 and ERF/DREB subfamily. All Motifs would play an important role in the combination of DNA recognition. A total of 204 AP2/EREBP transcription factors of Actinidia chinensis and 129 Arabidopsis AP2/EREBP transcription factor protein sequences were sequenced. The ERF subfamilies were further divided into B 1, B2, B3, B4, B5 and B6. DREB subfamilies were divided into A1, A2, A3, A4, A5 and A6. The phylogenetic analysis showed that the AP2 and RAV subfamily differentiated quite early and greatly. The ERF and DREB subfamily were closely located on the same branch and showed a shorter evolutionary history, which was consistent with the Arabidopsis AP2/EREBP subfamily classification, suggesting that the evolutionary pathways of AP2/EREBP family transcription factor in kiwifruit be similar to that of the Arabidopsis thaliana. When the Maplnspect tool was used to locate the 204 sequences of kiwifruit, it was found that the 204 sequences distributed on all the 29 chromosomes but number 10. The number of sequences distributed on the chromosomes varied from 1 to 24. Among them, 17 sequences distributed on number 3 and 14 on numberl4. The locations of 29 sequences still remained unclear. The secondary protein structure, protein tertiary structure and signal peptide of AP2/EREBP tran- scription factor of kiwifruit were analyzed by Protparam, SOPM, SWISS-MODEL and SignalP4.1 Sever. The results showed that the AP2/EREBP family proteins were rich in acidic amino acids and the theoretical isoelectric points of the most amino acids were within this acidic range. The secondary structure analysis showed that 23 amino acid sequences were composed of c^-helix, and the other amino acid sequences were β-sheet and β-turn, which scattered throughout the protein sequence. The tertiary structure predic- tion was very similar to that of Arabidopsis thaliana. Signal peptide analysis showed that only Achn132541 and Aehn240471 had signal peptides and the rest proteins did not exist in signal peptide, which belonged to non-secretory protein. The Illumia RNA-Seq data was downloaded from the EBI, un- der accession numbers GSE80565, GSE72806 and GSE67332. At the same time, the expression data of Arabidopsis homologous genes in each organ was downloaded from EMBI. The expression of homologous Arabidopsis gene was analyzed by MEV software. The results showed that these genes were highly induced by low temperature, high temperature, high salt and exogenous ABA treatment. They strongly ex- pressed in flower, fruit, leaf and root. [ Conclusion ]AP2/EREBP transcription factor was conservervative inevolutionary process, being involved in plant development and stress response regulation. AP2/EREBP transcription factor could be used to explore other function.
出处
《果树学报》
CAS
CSCD
北大核心
2017年第7期790-805,共16页
Journal of Fruit Science
基金
国家林业局948项目"猕猴桃新品种及分子育种研究技术引进"(2012-4-62)
云南省林学一流学科建设经费
云南省高校林木遗传改良与繁育重点实验室开放基金
西南林业大学大学生创新基金(C16063)
