Transcriptome profiles in E. coli under a prolonged starvation environment

How microorganisms resist nutrient-deficiency is important for understanding the pervasive prosperity of microbes in severe nutrient conditions. In laboratory culture, E. coli can survive for a long period of time under starvation, denoted as long-term stationary phase (LSP). Although physiology of those viable cells is of great interest, their genome-wide response has not yet been fully understood. In this study, we employed high-density oligonucleotide array to investigate the transcriptional profile of the cells exposed with supernatant of LSP culture. We compared the expression profiles of LSP to those of exponentially and short-term stationary phase, and revealed that the cellular physiology in the LSP environment is primarily represented by up-regulation of transporter genes and down-regulation of biosynthesis genes, which is similar to those in the short-term stationary phase. Our analysis further detected the differentially expressed functional gene categories between short- and long-term stationary phase, in terms of increasing the expressions of some stress-response genes and repressing the translational genes expressions, suggesting more survival/maintenance weighted metabolism in LSP. We also found the population-density-susceptible expression profiles in the LSP condition, which is also informative to understand the survival mechanism in long-term starvation. In total 23 samples; 5 different condtions (late-log in M63 glucose, short-term stationary phase in M63 glucose, glucose straved in M63, and long-term stationary phase in M63 glucose)