Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex

Deep conservation of ribosome stall sites across RNA processing genes

The rate of translation can vary depending on the mRNA template. During the elongation phase the ribosome can transiently pause or permanently stall. A pause can provide the nascent protein with the time to fold or be transported, while stalling can serve as quality control and trigger degradation of aberrant mRNA and peptide. Ribosome profiling has allowed for the genome-wide detection of such pauses and stalls, but due to library-specific biases, these predictions are often unreliable. Here, we take advantage of the deep conservation of protein synthesis machinery, hypothesizing that similar conservation could exist for functionally important locations of ribosome slowdown, here collectively called stall sites. We analyze multiple ribosome profiling datasets from phylogenetically diverse eukaryotes: yeast, fruit fly, zebrafish, mouse and human to identify conserved stall sites. We find thousands of stall sites across multiple species, with the enrichment of proline, glycine and negatively charged amino acids around conserved stalling. Many of the sites are found in RNA processing genes, suggesting that stalling might have a conserved role in RNA metabolism. In summary, our results provide a rich resource for the study of conserved stalling and indicate possible roles of stalling in gene regulation.

Non-tight and tight chemomechanical couplings of biomolecular motors under hindering loads

Biomolecular motors make use of free energy released from chemical reaction (typically ATP hydrolysis) to perform mechanical motion or work. An important issue is whether a molecular motor exhibits tight or non-tight chemomechanical (CM) coupling. The tight CM coupling refers to that each ATPase activity is coupled with a mechanical step, while the non-tight CM coupling refers to that an ATPase activity is not necessarily coupled with a mechanical step. Here, we take kinesin, monomeric DNA helicase, ring-shaped hexameric DNA helicase and ribosome as examples to study this issue. Our studies indicate that some motors such as kinesin, monomeric helicase and ribosome exhibit non-tight CM coupling under hindering forces, while others such as the ring-shaped hexameric helicase exhibit tight or nearly tight CM coupling under any force. For the former, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the CM coupling efficiency, while the ATPase rate is independent or nearly independent of the force. For the latter, the reduction of the velocity caused by the hindering force arises mainly from the reduction of the ATPase rate, while the CM coupling efficiency is independent or nearly independent of the force.

Mechanism of ribosome translation through mRNA secondary structures

A ribosome is a macromolecular machine that is responsible for translating the genetic codes in messenger RNA (mRNA) into polypeptide chains. It has been determined that besides translating through the single-stranded region, the ribosome can also translate through the duplex region of mRNA by unwinding the duplex. To understand the mechanism of ribosome translation through the duplex, several models have been proposed to study the dynamics of mRNA unwinding. Here, we present a comprehensive review of these models and also discuss other possible models. We evaluate each model and discuss the consistency and/or inconsistency between the theoretical results that are obtained based on each model and the available experimental data, thus determining which model is the most reasonable one to describe the mRNA unwinding mechanism and dynamics of the ribosome. Moreover, a framework for future studies in this subject is provided.

Processivity of nucleic acid unwinding and translocation by helicases

Helicases are a class of enzymes that use the chemical energy of NTP hydrolysis to drive mechanical processes such as translocation and nucleic acid (NA) strand separation. Besides the NA unwinding speed, another important factor for the helicase activity is the NA unwinding processivity. Here, we study the NA unwinding processivity with an analytical model that captures the phenomenology of the NA unwinding process. First, we study the processivity of the non-hexameric helicase that can unwind NA efficiently in the form of a monomer and the processivity of the hexameric helicase that can unwind DNA effectively, providing quantitative explanations of the available single-molecule experimental data. Then, we study the processivity of the non-hexameric helicases, in particular UvrD, in the form of a dimer and compare with that in the form of a monomer. The available single-molecule and some biochemical data showing that while UvrD monomer is a highly processive single-stranded DNA translocase it is inactive in DNA unwinding, whereas other biochemical data showing that UvrD is active in both single-stranded DNA translocation and DNA unwinding in the form of a monomer can be explained quantitatively and consistently. In addition, the recent single-molecule data are also explained quantitatively showing that constraining the 2B subdomain in closed conformation by intramolecular cross-linking can convert Rep monomer with a very poor DNA unwinding activity into a superhelicase that can unwind more than thousands of DNA base pairs processively, even against a large opposing force. Proteins 2016; 84:1590-1605. © 2016 Wiley Periodicals, Inc.

On the pathway of ribosomal translocation

The translocation of tRNAs coupled with mRNA in the ribosome is a critical process in the elongation cycle of protein synthesis. The translocation entails large-scale conformational changes of the ribosome and involves several intermediate states with tRNAs in different positions with respect to 30S and 50S ribosomal subunits. However, the detailed role of the intermediate states is unknown and the detailed mechanism and pathway of translocation is unclear. Here based on previous structural, biochemical and single-molecule data we present a translocation pathway by incorporating several intermediate states. With the pathway, we study theoretically (i) the kinetics of 30S head rotation associated with translocation catalyzed by wild-type EF-G, (ii) the dynamics of fluctuations between different tRNA states during translocation interfered with EF-G mutants and translocation-specific antibiotics, (iii) the kinetics of tRNA movement in 50S subunit and mRNA movement in 30S subunit in the presence of wild-type EF-G, EF-G mutants and translocation-specific antibiotics, (iv) the dynamics of EF-G sampling to the ribosome during translocation, etc., providing consistent and quantitative explanations of various available biochemical and single-molecule experimental data published in the literature. Moreover, we study the kinetics of 30S head rotation in the presence of EF-G mutants, providing predicted results. These have significant implications for the molecular mechanism and pathway of ribosomal translocation.

Model of the pathway of -1 frameshifting: Long pausing

It has been characterized that the programmed ribosomal -1 frameshifting often occurs at the slippery sequence on the presence of a downstream mRNA pseudoknot. In some prokaryotic cases such as the dnaX gene of Escherichia coli, an additional stimulatory signal-an upstream, internal Shine-Dalgarno (SD) sequence-is also necessary to stimulate the efficient -1 frameshifting. However, the molecular and physical mechanism of the -1 frameshifting is poorly understood. Here, we propose a model of the pathway of the -1 translational frameshifting during ribosome translation of the dnaX -1 frameshift mRNA. With the model, the single-molecule fluorescence data (Chen et al. (2014) [29]) on the dynamics of the shunt either to long pausing or to normal translation, the tRNA transit and sampling dynamics in the long-paused rotated state, the EF-G sampling dynamics, the mean rotated-state lifetimes, etc., are explained quantitatively. Moreover, the model is also consistent with the experimental data (Yan et al. (2015) [30]) on translocation excursions and broad branching of frameshifting pathways. In addition, we present some predicted results, which can be easily tested by future optical trapping experiments.

Model of the pathway of -1 frameshifting: Kinetics

Programmed -1 translational frameshifting is a process where the translating ribosome shifts the reading frame, which is directed by at least two stimulatory elements in the mRNA-a slippery sequence and a downstream secondary structure. Despite a lot of theoretical and experimental studies, the detailed pathway and mechanism of the -1 frameshifting remain unclear. Here, in order to understand the pathway and mechanism we consider two models to study the kinetics of the -1 frameshifting, providing quantitative explanations of the recent biochemical data of Caliskan et al. (Cell 2014, 157, 1619-1631). One model is modified from that proposed by Caliskan et al. and the other is modified from that proposed in the previous work to explain the single-molecule experimental data. It is shown that by adjusting values of some fundamental parameters both models can give quantitative explanations of the biochemical data of Caliskan et al. on the kinetics of EF-G binding and dissociation and on the kinetics of movement of tRNAs inside the ribosome. However, for the former model some adjusted parameter values deviate significantly from those determined from the available single-molecule experiments, while for the latter model all parameter values are consistent with the available biochemical and single-molecule experimental data. Thus, the latter model most likely reflects the pathway and mechanism of the -1 frameshifting.