Figure 1.
Growth of stationary phase culture of E. coli (O,•) and long-term stationary phase culture of E. coli which was held for 28 days at room temperature (□, ▪) that were sub-cultured for growth at 30°C in Luria-Bertani (LB) broth in the presence (O, □) and absence (•, ▪) of glycerol (10%).
Table 1.
Primers used for Real-Time PCR analysis of a few genes of E. coli.
Figure 2.
DNA microarray analysis of long-term stationary phase-induced gene expression in E. coli grown in LB broth.
The Volcano plot depicts gene expression in 28 days old E. coli culture at 0.8 OD (OD600nm) cultured in LB broth compared to the freshly grown stationary phase E. coli culture control. Genes that are represented on the right side of the volcano-axis are up regulated and those that are on left side of the axis are down regulated. Out of the 4377 genes (O) analysed, 25 genes were up-regulated (•) and 179 were down regulated (•). Only those genes that showed more than 2.0 fold change in expression and a P value <0.05 were identified as either up- or down-regulated. The X-axis represents the log2 fold change and the dark vertical lines represent cut-offs at 2.0 fold decrease and increase. The y-axis represents the p-values and the dark horizontal line indicates a –log10 p value cut-off of 0.05.
Figure 3.
Genes up regulated (%) in E. coli LSP cells compared with SP cells of E. coli which were both sub-cultured in LB based on biological process classification reported by Gene ontology term functional categories using DAVID version 2.0 software (A).
Genes down regulated (%) in E. coli LSP cells compared with SP cells of E. coli which were both sub-cultured in LB based on biological process classification reported by Gene ontology term functional categories using DAVID version 2.0 software (B).
Figure 4.
DNA microarray analysis of long-term stationary phase-induced gene expression in E. coli grown in LB broth plus glycerol.
The Volcano plot depicts gene expression in LSP E. coli culture at 0.8 OD (OD600nm) cultured in LB broth compared to the freshly grown SP E. coli culture l. Genes that are represented on the right side of the volcano-axis are up-regulated and those that are on left side of the axis are down-regulated. Out of the 4377 genes (O) analysed, 138 genes were up-regulated (•) and 183 were down-regulated (•). Only those genes that showed more than 2.0 fold change in expression and a P value <0.05 were identified as either up- or down-regulated. The X-axis represents the log2 fold change and the dark vertical lines represent cut-offs at 2.0 fold decrease and increase. The y-axis represents the –log10 p-values and the dark horizontal line indicates a p value cut-off of 0.05.
Figure 5.
Genes up regulated (%) in E. coli LSP cells grown in LB + glycerol compared with stationary phase cells of E. coli which was sub-cultured in LB based on biological process classification reported by Gene ontology term functional categories using DAVID version 2.0 software (A).
Genes down regulated (%) in E. coli LSP cells grown in LB + glycerol compared with stationary phase cells of E. coli which was sub-cultured in LB based on biological process classification reported by Gene ontology term functional categories using DAVID version 2.0 software (B).
Figure 6.
Real-Time PCR validation of the expression of insB, yhcE, ybfD, c3113, cysH, ydcC, oppA, csrC, dnaK, hdeA, ssrS, ryjA and aceB using RNA of LSP E. coli grown in LB broth (□) compared to stationary phase culture in LB broth (▪) (A).
Real-Time PCR validation of the expression of insB, yhcE, ybfD, c3113, cysH, ydcC, oppA, csrC, dnaK, hdeA, ssrS, ryjA and aceB using RNA of LSP E. coli grown in LB+glycerol (□) compared to stationary phase culture grown in LB+glycerol (▪) (B).
Table 2.
List of up-regulated genes in Escherichia coli due to long-term stationary phase effect.
Table 3.
List of down-regulated genes in Escherichia coli due to long-term stationary phase effect.