34 Cyo-EM visualization of Mycobacterium 70S ribosome reveals unique structural components at the function sites

The 3D structures of prokaryotic and eukaryotic ribosomes by crystallography and electron microscopy have revealed that they share an evolutionarily conserved core (Schmeing & Ramakrishnan, 2009), but each of the ribosomes contains its own set of specific proteins (or extensions of conserved proteins) and expansion segments of rRNAs (Melnikov et al., 2012). How these differences correlate to function still remains largely unknown. A 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis (Msm70S) unveiled striking new structural features (Shasmal & Sengupta, 2012). The core of the Msm70S shows overall similarity with the core of the Escherichia coli 70S ribosome while containing additional mass in the periphery and solvent exposed sides. Some of the Mycobacterium ribosomal proteins are significantly bigger as compared to the E. coli counter parts. The rRNAs also contain extra helices, also revealed by their secondary structures. Most of the additional density of the Msm70S can be largely attributed to the extra helices present in the rRNAs, and extra domains of homologous proteins. One of the most notable features appears in the large subunit near L1 stalk as a structure forming a long helix with its upper end located in the vicinity of the mRNA exit channel (which we term the ‘steeple’). We propose that the prominent helical structure in mycobacterium 23S rRNA participates in modulating different steps of translation, especially the E site tRNA exit mechanism and propagation of mRNA 5′ end.     

Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome

The ribosomal intersubunit bridges maintain the overall architecture of the ribosome and thereby play a pivotal role in the dynamics of translation. The only protein-protein bridge, b1b, is formed by the two proteins, S13 and L5 of the small and large ribosomal subunits, respectively. B1b absorbs the largest movement during ratchet-like motion, and its two proteins reorganize in different constellations during this motion of the ribosome.Our results in this study of b1b in the Escherichia coli 70S ribosome suggest that the intrinsic molecular features of the bridging proteins allow the bridge to modulate the ratchet-like motion in a controlled manner. Additionally, another large subunit protein, L31, seems to participate with S13 and L5 in the formation, dynamics, and stabilization of this bridge.     

Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features

Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria.