Showing papers by "Harry F. Noller published in 2022"

The role of GTP hydrolysis by EF-G in ribosomal translocation

Abstract: Significance Using ensemble FRET, we measured the effects of inhibition of GTP hydrolysis on rotational movements of the 30S ribosomal subunit and of the head domain of the 30S subunit during ribosomal translocation. Surprisingly, we find that blockage of GTP hydrolysis by the elongation factor G (EF-G) specifically abolishes reverse rotation of the head domain of the small ribosomal subunit, an event that occurs after translocation of the transfer RNA and messenger RNA is essentially complete. We propose that the principal role of GTP hydrolysis is to ensure that EF-G is not released from the ribosome until completion of each round of translocation, which guards against slippage of the translational reading frame.

The universally conserved nucleotides of the small subunit ribosomal RNAs

Abstract: The ribosomal RNAs, along with their substrates the transfer RNAs, contain the most highly conserved nucleotides in all of biology. We have assembled a database containing structure-based alignments of sequences of the small-subunit rRNAs from organisms that span the entire phylogenetic spectrum, to identify the nucleotides that are universally conserved. In its simplest (bacterial and archaeal) forms, the small-subunit rRNA has ∼1500 nt, of which we identify 140 that are absolutely invariant among the 1961 species in our alignment. We examine the positions and detailed structural and functional interactions of these universal nucleotides in the context of a half century of biochemical and genetic studies and high-resolution structures of ribosome functional complexes. The vast majority of these nucleotides are exposed on the subunit interface surface of the small subunit, where the functional processes of the ribosome take place. However, only 40 of them have been directly implicated in specific ribosomal functions, such as contacting the tRNAs, mRNA, or translation factors. The roles of many other invariant nucleotides may serve to constrain the positions and orientations of those nucleotides that are directly involved in function. Yet others can be rationalized by participation in unusual noncanonical tertiary structures that may uniquely allow correct folding of the rRNA to form a functional ribosome. However, there remain at least 50 nt whose universal conservation is not obvious, serving as a metric for the incompleteness of our understanding of ribosome structure and function.