Deconstructing ribosome construction

Abstract

The ribosome is an essential ribonucleoprotein enzyme, and its biogenesis is a fundamental process in all living cells. Recent X-ray crystal structures of the bacterial ribosome and new technologies have allowed a greater interrogation of in vitro ribosome assembly; however, substantially less is known about ribosome biogenesis in vivo. Ongoing investigations are focused on elucidating the cellular processes that facilitate biogenesis of the ribosomal subunits, and many extraribosomal factors, including modification enzymes, remodeling enzymes and GTPases, are being uncovered. Moreover, specific roles for ribosome biogenesis factors in subunit maturation are now being elaborated. Ultimately, such studies will reveal a more complete understanding of processes at work in in vivo ribosome biogenesis.

Figure 1

Bringing the maturation of ribosomal subunits into focus. Illustrated are the biogenesis pathways of the functional bacterial ribosomal subunits 30S (left; Protein Databank [PDB] code 2AVY; RNA colored gray and r-proteins colored blue) and 50S (right; PDB code 2AW4; RNA colored gray and r-proteins colored purple). The structures were generated using Pymol (http://pymol.sourceforge.net). The biogenesis of these subunits commences with transcription of primary rRNA transcripts, which contain 16S, 23S and 5S rRNA sequences and intervening sequences, and proceeds through a series of ill-defined stages. Although a precise X-ray crystal structure of the ribosomal subunits has been solved [–3], the cellular processes involved in ribosome maturation (presented within the gray box) remain incompletely understood. It is known that an array of ribosomal biogenesis factors facilitates processes through a coordinated series of maturation events. Some of these factors are listed in the middle of the gray box, but the temporal aspects of their function have not been resolved. Elucidating a more complete understanding of the specific processes involved in the biogenesis of ribosomes remains a formidable challenge in the field but would result in a lessening of the ‘gray haze’ overlaying the biogenesis cascade at this time.

Figure 2

Interaction map of 30S subunit components and a subset of biogenesis factors. Data derived from references herein, as well as recent large-scale protein interaction studies [80,81], reveal an interaction network of 30S subunit biogenesis factors, including endonucleases (red), ATPases (orange), rRNA and r-protein modification enzymes (blue), GTPases (green), other factors (purple) and yet to be identified factors (represented as various colored question marks). This map illustrates the complexity of the process and yet is still likely to be incomplete. Continued work on identifying biogenesis factors and characterizing their functions and interactions will shed light on both how and when biogenesis factors facilitate the maturation of ribosomal subunits.