Bioinformatics Prediction For Key Genes And Transcription Factors Of Protein Metabolism In Soybean

Nutritionally,proteins derived from soybean can be comparable with animal protein.Soybean protein is one of the main sources of protein nutrients for human beings.Several genes are involved in protein synthesis,transport,processing,utilization and degradation in the cell of soybean.Among these genes or transcript factors some,play a crucial role in protein metabolism.Currently,a lot of research focuses on gene function in soybean.Research on how genes participate in protein metabolism is still relatively low.This study focused on genes that participate in protein metabolism in soybeans.Therefore,from the perspective of soybean genome,we used genes that participate in the biosynthese of 21 kinds of amino acids in soybean as original gene.Then using co-expression analysis methods we screened out genes from soybean genome that has co-expression relationship with these original genes,we call these genes as purpose genes.Then we took pathway analysis on these purpose genes,and took GO analysis on homologs in Arabidopsis.We dug out genes in soybean that participate in the protein metabolism,to provide the theory reference for the genes related to protein metabolism in soybean cells.The main results of this study are as follows:1.Through searching the Soy-base,we obtained 455 genes that are related to the biosynthese of 21 kinds of amino acids in soybean.With the soybean transcriptome data sets from GEO database in NCBI,we screened out 5846 genes and 168 transcript factors from soybean genome that has obvious co-expression relationship(P<10-6)with these 455genes.2.Taking the Pathway analysis on these 5846 soybean genes,we dug out the other pathways that are indirectly involved in the biosynthese of amino acids.The results showed that Glyma02g01580 and other 48 genes may involved in glycolysis,TCA cycle,CO2 fixation into oxaloacetate,methylglyoxal degradation etc.These pathways are related with biosynthese of amino acids in soybean.Experiments have confirmed that these four genes:Glyma09g29840,Glyma12g0778,Glyma11g04720 and Glymal5g10070 really participate in their respective metabolic pathways.For example,Glyma09g29840 encoding(3-amylase,is a circumscribed amylase,it works from the non-reducing end,cut apart the a-1,4 bond in order,The hydrolysis products are all maltose.3.Through GO enrichment analysis for 2497 homologs from Arabidopsis,we screened out genes that may participate in the protein metabolism of soybean.Then we took functional annotations on these potential soybean genes.The results showed that Glyma17g31690 and other 21 genes may be involved in the process of amino acids transport to the ribosome.Proteins that are synthesized through free ribosome will be transported to chloroplasts and other organelles with the regulation of Glymal3g34080 and other 72 genes.Proteins that are synthesized through ribosome on endoplasmic reticulum will be folded with the regulation of Glyma01g22910 and other 77 genes,then be transferred to the Golgi apparatus via vesicles with the regulation of Glyma05g02980 and other 19 genes,finally complete the protein glycosylation with the regulation of Glyma14g14000 and other 20 genes.41 Arabidopsis genes are homologs of 56 soybean genes,functions of these genes in Arabidopsis have been confirmed with experiments.For example,AT5G05000 encoding chloroplast outer membrane translocation factor TOC34,it is receptor GTPase that located in chloroplast outer membrane.It can identify the signal peptide of the precursor protein,ensure the process of protein transporting to the chloroplast correctly.And Glyma03g00600 is homolog of AT5G05000.4.Through the annotation of co-expression transcript factor,we screened out Glyma19g37910 and other 8 key transcript factors that may regulate the protein metabolism from the 168 factors related with protein metabolism.For example,in Arabidopsis,AT2G36270 encoding ABI5,the over expression of ABI5 will depress the transcription of aspartate kinase,further influence the biosynthese of lysine.Soybean gene Glyma19g37910 from our research is homolog of AT2G36270.AT5G56860 encoding GNC,AT4G26150 encodingCGA1,their common effect regulate the biosynthese of glutamate.And Glyma13g00200 is homolog of AT5G56860,Glyma17g34670 is homolog of AT4G26150.These results supported that Glyma19g37910,Glyma13g00200 and Glyma17g34670 are key transcript factors that regulate the protein metabolism in soybean.Above results,Glyma02g01580 and other 275 genes in soybean perhaps are involved in the biosynthese of amino acids,protein transport,protein utilization,and protein degradation and so on.And these processes may be regulated by Glyma19g37910 and other 8 key transcript factors.