A Conundrum of r-Protein Stability: Unbalanced Stoichiometry of r-Proteins during Stationary Phase in Escherichia coli

Abstract

ABSTRACT Bacterial ribosomes are composed of three rRNA and over 50 ribosomal protein (r-protein) molecules. r-proteins are essential for ribosome assembly and structural stability and also participate in almost all ribosome functions. Ribosomal components are present in stoichiometric amounts in the mature 70S ribosomes during exponential and early stationary growth phases. Ribosomes are degraded in stationary phase; however, the stability and fate of r-proteins during stationary growth phase are not known. In this study, we report a quantitative analysis of ribosomal components during extended stationary-phase growth in Escherichia coli. We show that (i) the quantity of ribosomes per cell mass decreases in stationary phase, (ii) 70S ribosomes contain r-proteins in stoichiometric amounts, (iii) 30S subunits are degraded faster than 50S subunits, (iv) the quantities of 21 r-proteins in the total proteome decrease during 14 days (short-lived r-proteins) concomitantly with the reduction of cellular RNA, and (e) 30 r-proteins are stable and form a pool of free r-proteins (stable r-proteins). Thus, r-proteins are present in nonstoichiometric amounts in the proteome of E. coli during the extended stationary phase. IMPORTANCE Ribosome degradation has been extensively described from the viewpoint of its main component, rRNA. Here, we aim to complement our knowledge by quantitatively analyzing r-protein degradation and stability both in the ribosomes and in the whole-cell proteome during stationary phase in E. coli. r-proteins are considered to be very stable in the proteome. Here, we show that a specific set of r-proteins are rapidly degraded after release from the rRNA. The degradation of r-proteins is an intriguing new aspect of r-protein metabolism in bacteria.

Keywords

• proteomics
• rRNA
• ribosomal proteins
• ribosomes
• stationary phase