Research On The Molecular And Physiological Levels Of Escherichia Coli K12-NCM3722 In The Logarithmic And Stationary Phase

With the popularity of high-throughput second-generation sequencing technology,people can understand the nature of biogenesis from the level of total transcription.In addition,other omics studies including genomics,proteomics,and metabolomicsare also applied frequently to reveal the nature of biology.Therefore,modern biological research tends to involve big data analysis and studies biological phenomena systemticly.This article studied transcriptome,metabolome,viable count,stress tests,and total protein,total RNA,total DNA quantification on an E.coli wild-type strain,NCM3722,grown at logarithmic phase[OD₆₀₀=0.4?middle logarithmic phase,stat1?;OD₆₀₀=0.7(end of logarithmic phase,stat2]and grown at stationary phase[cultured for 24h?stat3?,cultured for 48h?stat4?,cultured for 72h?stat5?]in order to systematicly reveal the difference between bacteria grown at logarithmic phase and stationary phase from the molecular level to the physiological level.The total number of genes determined by RNA deep sequencing was 4534.Gene expression clustering analysis and differential expressed gene analysis showed that there was no significant difference in gene expression levels among stat3,stat4,and stat5,but significant difference in gene expression were found among stat1,stat2 and stat3.Then analysis of gene expression trend following growth stages were performed and four major expression profiles were identified,namely profile0?straight down?,profile3?flat down?,and profile4?flat up?,profile7?straight up?.And gene numbers in the four profiles were 760,718,323,and 103,individually.GO term analysis and KEGG Pathway enrichment analysis were done for the genes in each profile.Pathways of profile0,profile3,profile4,profile7 were individually significantly enriched in ribosomes,amino acid metabolism,two-component systems and ABC transporters.We applied non-targeted GC-MS to study the metabolic profiling of both bacteria ?metabolome?and supernatants from bacterial culture media?exo-metabolome?.181and 175 metabolites were identified respectively in metabolome and exo-metabolome.89 metabolites were found in both metabolome and exo-metabolome.Analysis of metabolite changing trend following growth stages suggested that the significant trends of both metabolome and exo-metabolome were the same,namely Profile3?straight down?,Profile4?flat up?,and Profile7?straight up?.Majority of metabolites showing big fold changes in Profile3 included sugar,sugar alcohol,and sugar acid.Metabolites appeared in Profile4 were mainly amino acid,amino acid derivatives,purine and pyrimidine.Metabolites identified in Profile7 showed similar functions to those in Profile4.CFU?CFU/OD?study revealed that there was no difference between stat1 and stat2,but there was significant difference between stat1,stat2 and stat3,stat4,stat5,which was in consistent with the growth curve of bacteria.Stress tests showed that bacteria grown in stationary phase?stat3?was more resistent to oxidative stress and osmotic stressthan bacteria grown in logarithmic phase?stat1?,which was in consistent with the transcriptome data in which the expression of stress-related genes increased during stationary phase.In addition,the amount of total DNA of the bacteria grown at the logarithmic phase?stat1,stat2?was significantly less than the bacteria grown at the stationary phase?stat3,stat4,stat5?,but he amount of total RNA of the bacteria grown at the logarithmic phase?stat1,stat2?was significantly higher than the bacteria grown at the stationary phase?stat3,stat4,stat5?.In contrast,total protein content showed no difference for the bacteria grown at difference growth stages.