Ribosome heterogeneity: another level of complexity in bacterial translation regulation

Abstract

Translation of the mRNA-encoded genetic information into proteins is catalyzed by the intricate ribonucleoprotein machine, the ribosome. Historically, the bacterial ribosome is viewed as an unchangeable entity, constantly equipped with the entire complement of RNAs and proteins. Conversely, several lines of evidence indicate the presence of functional selective ribosomal subpopulations that exhibit variations in the RNA or the protein components and modulate the translational program in response to environmental changes. Here, we summarize these findings, which raise the functional status of the ribosome from a protein synthesis machinery only to a regulatory hub that integrates environmental cues in the process of protein synthesis, thereby adding an additional level of complexity to the regulation of gene expression.

Figure 1

Known and predicted mechanisms underlying ribosome heterogeneity in E. coli. Intrinsic ribosome heterogeneity under relaxed conditions could be attributed to (i) the presence of seven rrn operons that slightly differ in sequence (sequence micro-heterogeneity; indicated by different colors of the arrows representing the rrn operons; not drawn to scale), and (ii) diverse modifications of the 16S rRNA (indicated by stars) or (iii) the assembly of modified r-proteins (indicated by dots) during ribosome biogenesis. However, as the expression of the rrn operons as well as of the modifying enzymes can be affected by external signals, these mechanisms could likewise result in induced ribosome heterogeneity, thereby specifically adapt translational activity and/or specificity to environmental conditions. In response to stress conditions ribosomes can be altered by (iv) conditional modification of the rRNA either during ribosome biogenesis [47] or on mature ribosomal subunits [48], (v) removal [28] or exchange of r-proteins by a mechanism shown by [39], and by (vi) the truncation of the 16S rRNA via the stress-induced endoribonuclease MazF [34^••]. Mechanisms that contribute to the generation of heterogeneity during biogenesis are depicted by straight arrows, whereas circular arrows indicate the alteration of mature ribosomes.

Figure 2

The ‘hot spots’ of induced ribosome heterogeneity. Structure of the 30S subunit from the solvent side (a), rotated about 90° around the vertical axis (b), and from the subunit interface (c). The stoichiometry of r-proteins S1 (tentative binding site on the ribosome is indicated by a blue circle), S2 (blue), S6 (purple), S12 (green), S18 (pink), and S21 (yellow) is affected in response to environmental cues or by the presence of the aminoglycoside antibiotic kasugamycin [5,7,28]. Nucleotides 1500–1542 of the 16S rRNA (termed ‘RNA43’ when cleaved off by MazF) are shown in magenta. Other r-proteins and the 16S rRNA are shown in gray. The structure was modeled using Polyview 3D molecular system software [52] and PDB file 2AVY [53].

Figure 3

MazF-dependent generation of stress-ribosomes. (a) The secondary structure of the Escherichia coli 16S rRNA is depicted. The helices 44 and 45 are enlarged, the ACA-site is indicated in magenta and the position of MazF cleavage between nucleotides A1499 and A1500 is indicated by an arrow. (b) The structure of the 30S subunit as seen from the solvent side. The tRNAs are shown in black, and the mRNA bound to the ribosomal subunit is shown in green. RNA43 of the 16S rRNA, which is removed upon MazF cleavage (shown in magenta), interacts via formation of the Shine and Dalgarno duplex with the mRNA. The structure was modeled using Polyview 3D molecular system software [52] and PDB file 2HGP [54].