Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle

Abstract

Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.

Network theory of the bacterial ribosome

“…The observed changes in the density and assortativity between the subunit and the entire structure, due to the intersubunit bridges, highlights the pivotal role of dynamics in the analysis. It hints that communication in this context may be dominated by mechanics, vibrational motions and allosteric pathways [ 30 – 32 , 40 ].…”

“…The observed changes in the density and assortativity between the subunit and the entire structure, due to the intersubunit bridges, highlights the pivotal role of dynamics in the analysis. It hints that communication in this context may be dominated by mechanics, vibrational motions and allosteric pathways [30][31][32]40]. In the first series we included all interactions and in the second we excluded all rRNA interactions, in the third we exclude all rprotein interactions.…”

“…Other important techniques explore the effects of antibiotics [ 19 , 26 ] and/or the creation of mutant rproteins with specific residues removed [ 27 – 29 ]. Explorations of allostery [ 30 – 32 ], ribosome heterogeneity and specialization [ 33 , 34 ] have provided important new insights into communication and signaling. Since many interactions are determined during ribosome biogenesis, it is also likely that their role in this process is related to functionality during translation.…”

Ribosomal protein eL24, involved in two intersubunit bridges, stimulates translation initiation and elongation

“…eEF2-dependent step is accompanied by the back-rotation of the 40S subunit relative to the 60S subunit (11,36,54). Interestingly, resent study has revealed the communication pathway between the eEF2 binding site and the 40S subunit through the rearrangement of the eB13 bridge (56). Altogether, reduced elongation rate reflects the involvement of eB13 bridge in the maintenance of ribosome conformation by controlling the ribosome subunit rotation during elongation cycle.…”

Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives

“…However, this sequence is certainly of a more elaborate nature than a pure TASEP, needing the intervention of external factors for regulation and also an internal control and adaptation, probably helped by the rRNA, mRNA, tRNA and the r-proteins. Interestingly, remote communication processes have been recently shown to participate in the coordination of complex ribosomal movements during translation [29,30], thus suggesting that ribosomal motions may be helped by external synchronization systems.…”