Growth phase-coupled changes of the ribosome profile in natural isolates and laboratory strains of Escherichia coli

The growth phase-dependent change in sucrose density gradient centrifugatio n patterns of ribosomes was analyzed for both laboratory strains of Escheri chia coli and natural isolates from the ECOR collection. All of the natural isolates examined formed 100S ribosome dimers in the stationary phase, and ribosome modulation factor (RMF) was associated with the ribosome dimers i n the ECOR strains as in the laboratory strain W3110. The ribosome profile (70S monomers versus 100S dimers) follows a defined pattern over time durin g lengthy culture in both the laboratory strains and natural isolates. Ther e are four discrete stages: (i) formation of 100S dimers in the early stati onary phase; (ii) transient decrease in the dimer level; (iii) return of di mers to the maximum level; and (iv) dissociation of 100S dimers into 70S ri bosomes, which are quickly degraded into subassemblies. The total time for this cycle of ribosome profile change, however, varied from strain to strai n; resulting in apparent differences in the ribosome profiles when observed at a fixed time point. A correlation was noted in all strains between the decay of 100S ribosomes and the subsequent loss of cell viability. Two type s of E. coli mutants defective in ribosome dimerization were identified, bo th of which were unable to survive for a prolonged period in stationary pha se. The W3110 mutant, with a disrupted rmf gene, has a defect in ribosome d imerization because of lack of RMF, while strain Q13 is unable to form ribo some dimers due to a ribosomal defect in binding RMF.