ABSTRACT
Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates.
Subject(s)
Ribosomal Proteins/metabolism , Ribosome Subunits, Small, Bacterial/metabolism , Ribosome Subunits, Small, Bacterial/ultrastructure , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Image Processing, Computer-Assisted , Kinetics , Mass Spectrometry , Microscopy, Electron/methods , Models, Molecular , Nucleic Acid Conformation , Protein Binding , Protein Conformation , RNA, Bacterial/chemistry , RNA, Ribosomal/chemistry , Ribosomal Proteins/chemistry , Ribosome Subunits, Small, Bacterial/chemistryABSTRACT
Although high-resolution structures of the ribosome have been solved in a series of functional states, relatively little is known about how the ribosome assembles, particularly in vivo. Here, a general method is presented for studying the dynamics of ribosome assembly and ribosomal assembly intermediates. Since significant quantities of assembly intermediates are not present under normal growth conditions, the antibiotic neomycin is used to perturb wild-type Escherichia coli. Treatment of E. coli with the antibiotic neomycin results in the accumulation of a continuum of assembly intermediates for both the 30S and 50S subunits. The protein composition and the protein stoichiometry of these intermediates were determined by quantitative mass spectrometry using purified unlabeled and (15)N-labeled wild-type ribosomes as external standards. The intermediates throughout the continuum are heterogeneous and are largely depleted of late-binding proteins. Pulse-labeling with (15)N-labeled medium time-stamps the ribosomal proteins based on their time of synthesis. The assembly intermediates contain both newly synthesized proteins and proteins that originated in previously synthesized intact subunits. This observation requires either a significant amount of ribosome degradation or the exchange or reuse of ribosomal proteins. These specific methods can be applied to any system where ribosomal assembly intermediates accumulate, including strains with deletions or mutations of assembly factors. This general approach can be applied to study the dynamics of assembly and turnover of other macromolecular complexes that can be isolated from cells.
Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Proteome/analysis , RNA, Ribosomal/metabolism , Ribosomal Proteins/metabolism , Ribosomes/metabolism , Escherichia coli/drug effects , Neomycin/pharmacology , Protein Synthesis Inhibitors/pharmacology , Proteome/drug effects , RNA, Ribosomal/chemistry , RNA, Ribosomal/genetics , Ribosome Subunits, Large, Bacterial/chemistry , Ribosome Subunits, Large, Bacterial/metabolism , Ribosome Subunits, Small, Bacterial/chemistry , Ribosome Subunits, Small, Bacterial/metabolism , Ribosomes/chemistry , Spectrometry, Mass, Electrospray IonizationABSTRACT
The Escherichia coli 30S ribosomal subunit self-assembles in vitro in a hierarchical manner, with the RNA binding by proteins enabled by the prior binding of others under equilibrium conditions. Early 16S rRNA binding proteins also bind faster than late-binding proteins, but the specific causes for the slow binding of late proteins remain unclear. Previously, a pulse-chase monitored by quantitative mass spectrometry method was developed for monitoring 30S subunit assembly kinetics, and here a modified experimental scheme was used to probe kinetic cooperativity by including a step where subsets of ribosomal proteins bind and initiate assembly prior to the pulse-chase kinetics. In this work, 30S ribosomal subunit kinetic reconstitution experiments revealed that thermodynamic dependency does not always correlate with kinetic cooperativity. Some folding transitions that cause subsequent protein binding to be more energetically favorable do not result in faster protein binding. Although 3(') domain primary protein S7 is required for RNA binding by both proteins S9 and S19, prior binding of S7 accelerates the binding of S9, but not S19, indicating there is an additional mechanistic step required for S19 to bind. Such data on kinetic cooperativity and the presence of multiphasic assembly kinetics reveal complexity in the assembly landscape that was previously hidden.
