关键词: RNA-Seq, 外源糖, 蛋白激酶, 信号转导

Abstract:

【Objective】 To explore the effects of different exogenous sugars on the growth and development of grape plantlets and the regulation of protein kinase gene transcription, the candidate genes were tapped in the process of protein phosphorylation by using transcription, which made a foundation for the verification of grape protein kinase-related gene function.【Method】 Sucrose (2%), glucose (2%) and fructose (2%) were added to the basic medium, and the free-sugar treatment was as control, which were named as S20, G20, F20 and CK, respectively. After 37 days of culture, the fresh weight of the leaf-stem and root under different treatments was determined. Transcriptome sequencing of each treated foliages was performed by using Illumina HiSeq ^TM 2000, and a series of protein kinases related genes were screened by integrated bioinformatics analysis, including reference genomic alignment, differentially expressed gene (DEGs) screening, COG (Cluster of Orthologous Groups of proteins) annotation, GO (Gene Ontology) annotation, etc., and the expression characteristic of these genes were further analyzed by qRT-PCR. 【Result】 Compared with CK, ‘Red Globe’ grape plantlets under F20, G20 and S20 treatments exhibited significant differences in the fresh weight of leaf-stem, and the highest was obtained by F20 treatment, while the weight of fresh root under G20 was the highest. The SNP statistics found that the Transition was the main type of mutation, the second was Transversion. The highest number of SNPs that occurred in the Intergenic, and the next was the Upstream. Splice_Site_Donor and Synonymous_Stop events occurred with the least number of genes and equal. A total of 2 633 deferentially expressed genes were obtained in the 4 samples. The Venn diagram showed that there were a total of 180 differential genes under the 3 treatments compared with CK, and these genes were clustered into 3 groups. In the first group, 127 genes were only highly expressed under CK. The 19 genes of the second group were only highly expressed under G20, while the expression patterns of the 34 genes in third group were different under three treatments. The common 180 differential genes were annotated with 26 genes in the COG database to 11 functional categories, and these DEGs were mainly enriched in general functional categories. In the annotation of GO, the common genes were annotated in 14, 22 and 13 functional categories of molecular function, biological process and cellular component, respectively. Seven kinds of protein kinases were screened by this sequencing, including Glucokinase (GK), Mitogen-activated protein kinases (MAPKs), Calcineurin protein kinase (CBL), Protein phosphatase 2 (PP2A), Hexokinase (HXK), Histidine protein kinase (HPK) and Tyrosine kinase (TK), and these different protein kinases genes showed their own expression patterns among different treatments. By qRT-PCR analysis, 17 out of 20 screened genes expression were consistent with the transcriptome sequencing results. 【Conclusion】 Compared with glucose and sucrose, fructose was the best sugar during grape culture process. The sequencing results showed that 180 DEGs all responded to three different sugars. In the COG annotation, these genes were mainly enriched in membrane ester transport and metabolism, the synthesis, transport and decomposition of secondary metabolites and carbohydrates. In the GO databases, the most of common DEGs were annotated in the activities of protein kinases and oxidoreductases. Seven protein kinases were identified, which were selectively in responses to different exogenous sugars in quantity, functional, category and metabolic pathways, and had their own choice of expression specificity.

Key words: RNA-seq, exogenous sugar, protein kinase, signaling transduction