Selective Reprogramming of Ribosome Assembly and Translational Control during Bacterial Growth Phase Transitions

Abstract

Most bacteria in natural environments experience prolonged nutrient limitation resembling the stationary phase and only intermittently encounter nutrient-rich conditions analogous to exponential growth. Understanding the molecular processes operating in these two states is therefore essential for elucidating bacterial adaptation to fluctuating nutrient availability. We applied a label-free proteomics workflow to characterize protein-level differences in the Escherichia coli (E. coli) proteome between exponential and prolonged stationary growth phases. We found that multiple components of the translational machinery are selectively enriched during the exponential growth. These include the DEAD-box rRNA (rRNA) chaperones DeaD, DbpA, and RlhE, the small-subunit ribosomal protein chaperone RimP, and 13 ribosomal proteins, several of which possess RNA and/or combined RNA-protein chaperone activity. In addition, enzymes responsible for post-transcriptional modification of rRNA and tRNA, RlmN, RsmI, RluB, RlmG, and TsaC, were more abundant during exponential growth, consistent with enhanced ribosome stability, translation rate, and translational fidelity under conditions of rapid proliferation. Translation initiation factors IF-1 and IF-3 and the elongation factor EF-P, which support efficient translation initiation and alleviate ribosomal stalling on challenging sequences, were also elevated during the exponential phase. Finally, a distinct set of proteins associated with antibiotic response exhibited differential abundance between exponential and stationary growth phases, indicating growth phase-dependent remodeling of cellular stress and defense pathways. Together, these findings provide a statistically supported, protein-level framework that defines how specific components of the translational machinery are selectively remodeled during the transition between exponential and stationary growth phases in E. coli, with potential relevance to other bacteria.