Evolutionary Origins of Ribosome Dynamics

The modern ribosome is a dynamic molecular machine comprised of RNA and protein. It is responsible for all coded protein synthesis. A growing peptide is synthesized one residue at a time and when complete it is released from the ribosome. During each round of synthesis, the ribosome itself undergoes a cycle of motions, which facilitate the synthesis and ultimately restore the ribosome to its original state. In recent years, it has become possible to determine the structure of the ribosome at atomic resolution at each individual state using electron microscopy and/or cryoelectron microscopy. Comparison of structures between states allows one to identify pivot points where motion appears to originate. Separately, a variety of techniques have been developed that allow assessment of the relative age of various regions of the ribosomal RNA. In particular, it is found that the RNA likely grew in complexity by accretion over evolutionary time. In essence, new RNA is added to existing RNA without disrupting the previous structure. Thus, each helix is grouped into one of six phases ranging from ancient to most recent. Thus, the relative age of each pivot point that was associated with ribosome motion could be identified. The oldest helices associated with motion were not associated with the EF-Tu/EF-G binding site as one might have expected. Instead, it is helices h28 and h44, which comprise part of the decoding region that appear to be the oldest. It is speculated that the combination of these two structural elements would be inherently dynamic even in the absence of the ribosome.

 

Bowman, J.C., Petrov, A.S., Frenkel-Pinter, M., Penev, P.I., and Williams, L.D. "Root of the Tree: The Significance, Evolution, and Origins of the Ribosome", Chemical Reviews 120, 4848-4878 (2020) doi.org/10.1021/acs.chemrev.9b00742
 

Relevant Reading Material

Paci M & Fox GE. (2016) Centers of motion associated with EF-Tu binding to theRibosome. RNA Biology; 13: 524-530. PMID 26786136.

Paci M & Fox GE. (2015) Major centers of motion in the large ribosomal RNAs. Nucleic Acids Research 43: 4640-4649.

Petrov AS, Bernier CR, Hsiao C, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG,Harvey SC, Fox GE, Wartell, RM, Hud NV, & Williams LD. Evolution of the ribosome at atomic resolution. Proc Natl Acad Sci USA 111: 10251-10256 (2014).

Illustration of rRNA pivots points. The arrows diverge from one another at the pivot point.