Preliminary Construction And Analysis Of Acid-tolerant Network Of Lactococcus Lactis And Escherichia Coli

Industrial microorganisms can acidify the fermentation environment due to the accumulation of acid metabolites during fermentation,and pathogenic bacteria must be in the face of acid stress from the gastrointestinal tract and phagosome so that can survive in the host.Therefore,it is particularly important to analyze acid tolerance of industrial microorganisms and pathogenic bacteria.By using the method of scientific quantitative analysis,the co-occurrence of acid-tolerant keywords were analyzed in 6012 and 582 microbial acid-tolerant literatures from PubMed and CNKI database,and 14 industrial microorganisms,16 pathogenic bacteria and 21 acidophilic bacteria were obtained.16 S rRNA phylogenetic tree of was constructed,and it was found that these bacterias had close evolutionary relationships and phenomena of horizontal gene transfer might exist among acid-tolerant elements.L.lactis F44 was used as the research material for acid tolerance of industrial microorganisms.iTRAQ proteomic analysis was performed after acid stress of L.lactis F44.115 DEPs were up-regulated,45 differentially expressed proteins(DEPs)were down-regulated after acid stress of pH4.The metabolic pathways involved in these DEPs include transcriptional regulators,DNA and protein repair,ribosomal synthetic proteins,transporters and stress responses,and construct the PPI networks of these DEPs.Unknown function protein YxbF interacts with stress protein YxbE.Bioinformatics prediction of its function were made in the aspects of hydrophobicity,transmembrane region,glycosylation and phosphorylation sites and tertiary structure.The PPI network of L.lactis F44 is reconstructed with Cytoscape 3.6.1.MCODE analyses the network structure and obtains 8 modules with statistical significance,including 2 high connectivity networks,2 medium connectivity networks and 4smaller PPI networks.E.coli K12 was used as research material for acid tolerance of pathogenic bacteria.The expression profiles of GSE4511,GSE4556,and GSE4778 were downloaded from the GEO database.The three microarray datasets were integrated to obtain differentially expressed genes(DEGs)and were deeply analyzed by bioinformatics methods.The top-50 upregulated or downregulated genes among DEGs were identified from the GSE4511,GSE4556,and GSE4778 datasets.The PPInetwork of the DEGs was constructed from the STRING database.A total of 52 DEGs were identified in the three GEO datasets,of which 32 genes were upregulated and 20 genes were downregulated.Furthermore,gene set enrichment analysis(GSEA)demonstrated that there was no significant change in important metabolic pathways that might be involved in acid stress,i.e.KEGG_Non-coding RNAs.The PPI network of E.coli K12 is reconstructed with Cytoscape 3.6.1.MCODE analyses the network structure and obtains 3 high connectivity networks,6 medium connectivity networks and 12 smaller PPI networks.In conclusion,we screened microbial acid resistant DEGs or DEPs,taking L.lactis F44 and E.coli K12 as the research objects,through bibliometric analysis of acid resistant research literature,iTRAQ proteomics and analysis of gene chip based on GEO database and PPI network based on STRING database.This study indicates that screening for DEGs or DEPs and pathways using integrated bioinformatics analyses could help us understand the molecular mechanism underlying the acid tolerance of microorganism,and provide effective ideas for construction of acid-tolerant genetic engineering bacteria and the treatment of diseases caused by foodborne pathogenic bacteria.