Genome-wide bioinformatics analysis of AP2/EREBP transcription factor in‘Hongyang’kiwifruit

Abstract:【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 oneAP2 binding domain and about 60-70 highly conserved amino acids. The function of the AP2/EREBPtranscription factor family of the genome of Actinidia chinensis was analyzed with the completion of sequencing of the full genome of‘Hongyang’kiwifruit.【Methods】AP2/EREBP family transcription factorswere 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. Andthe 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 byMEME. In order to analyze the evolutionary relationship of 204 AP2/EREBP transcription factors in‘Hongyang’kiwifruit, ClustalX2 and MEGA6.0 were used to sequence the AP2/EREBP transcripts of Actinidiachinensis and Arabidopsis thaliana, and to carry out the phylogenetic analysis. The Physicochemical properties, secondary structure, tertiary structure, and signal peptide analysis of the AP2/EREBP transcriptionfactor protein sequence of Actinidia chinensis were carried out using Protparam, SOPM, SWISS-MODELand SignalP4.1 Sever. The Kiwifruit AP2/EREBP transcription factor sequence information was obtainedfrom 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 BioEditsoftware. 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 inthe 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 DREBby 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“Vac14_Fab1_bd”domains. Sequence element analysis showed that Motif1 belongedto the AP2 domain, Motif2, and Motif3 belonged to the B3 domain of RAV subfamily. Motif1, Motif2 andMotif3 belonged to the AP2 domain of AP2 and ERF/DREB subfamily. All Motifs would play an importantrole in the combination of DNA recognition. A total of 204 AP2/EREBP transcription factors of Actinidiachinensis and 129 Arabidopsis AP2/EREBP transcription factor protein sequences were sequenced. TheERF subfamilies were further divided into B1, B2, B3, B4, B5 and B6. DREB subfamilies were divided in⁃to A1, A2, A3, A4, A5 and A6. The phylogenetic analysis showed that the AP2 and RAV subfamily differ⁃entiated quite early and greatly. The ERF and DREB subfamily were closely located on the same branchand showed a shorter evolutionary history, which was consistent with the Arabidopsis AP2/EREBP sub⁃family classification, suggesting that the evolutionary pathways of AP2/EREBP family transcription factorin kiwifruit be similar to that of the Arabidopsis thaliana. When the MapInspect tool was used to locate the204 sequences of kiwifruit, it was found that the 204 sequences distributed on all the 29 chromosomes butnumber 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 number14. The locations of 29 sequences still remainedunclear. The secondary protein structure, protein tertiary structure and signal peptide of AP2/EREBP transcription 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 theoreti⁃cal isoelectric points of the most amino acids were within this acidic range. The secondary structure analy⁃sis showed that 23 amino acid sequences were composed of α-helix, and the other amino acid sequenceswere 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 onlyAchn132541 and Achn240471 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, under accession numbers GSE80565, GSE72806 and GSE67332. At the same time, the expression data ofArabidopsis homologous genes in each organ was downloaded from EMBI. The expression of homologousArabidopsis 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 expressed in flower, fruit, leaf and root.【Conclusion】AP2/EREBP transcription factor was conservervative in evolutionary process, being involved in plant development and stress response regulation. AP2/EREBPtranscription factor could be used to explore other function.