Bioinformatics Analysis Of The RWP-RK Transcription Factor And The Protein Phosphatase Gene Families In Oomycetes

Phytophthora sojae infects soybeans and causes soybean root rot,which seriously affects soybean yield and quality.Phytophthora sojae belongs to the oomycetes of the Stramenopila.Although the mycelial properties of the vegetative oomycetes are similar to those of fungi,but they are related to algae such as brown algae and diatom in evolution.Such differences result in many differences between Phytophthora sojae and fungi in terms of genomic composition,metabolic pathway and pathogenic mechanism.Therefore,it is of great significance to study the molecular mechanism of Phytophthora disease for the development of disease control strategies and technologies.Regulation of gene expression is an important biological regulatory process of pathogens,transcription factors,protein kinases and phosphatases play important regulatory roles in gene transcription process and signal transmission process of organisms,respectively.In this study,we conducted a series of bioinformatics analysis and preliminary research on the functions of two regulatory factors,RWP-RK transcription factor family and protein phosphatase family in oomycetes.The main research contents are as follows:Genome-wide analysis of the RWP-RK transcription factor family.RWP-RK is a family of transcription factors commonly found in eukaryotes.Its protein sequence contains a conserved RWPXRK motif,which exist in all vascular plants,green algae and Dictyostelium cyclic,and therefore considered a plant specific transcription factor family.In this study,through bioinformatics analysis of the whole genomes of different representative species,it was found that RWP-RK protein is also widely present in the Stramenopila kingdom,especially in oomycetes,each species has 12-15 members.These proteins form three distinct phylogenetic subsets,two of which are closely related to the NLP or RKD subfamily of plant RWP-RK proteins.The donor of RWP-RK domain level gene transfer to Dictyostelium cyclic was most likely from the Stramenopila,which occurred before the differentiation of brown algae and oomycetes.Plant and oomycetes RWP-RK proteins have conserved secondary structures,but there are differences in individual amino acid sites related to DNA binding specificity.The RWP-RK direct homologous genes between Phytophthora sojae and Pythium ultimum have similar transcription patterns.Our results suggest that "plant-specific" RWP-RK transcription factor are also widespread in oomycetes,and some form specific subsets with conserved functions.These results provide new clues for further understanding the evolution and function of this transcription factor family in eukaryotes.Genome-wide search and analysis of phosphatase family.Protein phosphatase is an enzyme that dephosphorylates a corresponding substrate.It classified differently in fungi,plants,and mammals.This study first focused on the differences and connections between different species of protein phosphatase and different families of the same species,sorted out a set of systematic classification methods of protein phosphatase,and provided the corresponding Pfam ID number of each protein phosphatase family.Based on these Pfam ID numbers,the HMM models of different families of protein phosphatases were downloaded and the sequences of protein phosphatases of different species were searched by HMMER program.Then the identified protein phosphatases corrected by Pfam A database.According to the classification standard of fungi,the predicted oomycetes protein phosphatase divided into PTP,HP,PPPL and PPM families.The results showed that there were significant differences in the number of phosphatase proteins between oomycetes and fungi,such as 173 phosphatase proteins in Phytophthae sojae,186 phosphatase proteins in Phytophthora infestans,167 phosphatase proteins in Phytophthae capsici,etc.Among fungi,Magnaporthe oryzae had 70 protein phosphatases,Fusarium graminearum had75 protein phosphatases,and Saccharomyces cerevisiae had 68 protein phosphatases.After studying the phylogenetic relationships of different protein phosphatase families,this study focused on PP2 C of the oomycetes PPM family,and analyzed the taxonomic and structural characteristics of PP2 C of Phytophthae sojae.Subsequently,we obtained three knockout transformants of Ps PP2 C.Analysis showed that Ps PP2 C was involved in the process of mycelial growth and sporangium production,the virulence and production of oospores decreased of the Ps PP2 C knockout mutant in Phytophthae sojae.Phosphatase and transcription factors are important regulatory factors of biological signal transduction and transcriptional regulation respectively,which play important biological functions in the growth,development and pathogenicity of plant pathogens.In this study,the protein phosphatase family and the RWP-RK transcription factor family of oomycetes analyzed by bioinformatics and their functions were preliminary studied,which laid a foundation for the subsequent identification and functional genomics research of these genes.