-
PloS One 2020In the past two decades, research into the biochemical, biophysical and structural properties of the ribosome have revealed many different steps of protein translation....
In the past two decades, research into the biochemical, biophysical and structural properties of the ribosome have revealed many different steps of protein translation. Nevertheless, a complete understanding of how they lead to a rapid and accurate protein synthesis still remains a challenge. Here we consider a coarse network analysis in the bacterial ribosome formed by the connectivity between ribosomal (r) proteins and RNAs at different stages in the elongation cycle. The ribosomal networks are found to be dis-assortative and small world, implying that the structure allows for an efficient exchange of information between distant locations. An analysis of centrality shows that the second and fifth domains of 23S rRNA are the most important elements in all of the networks. Ribosomal protein hubs connect to much fewer nodes but are shown to provide important connectivity within the network (high closeness centrality). A modularity analysis reveals some of the different functional communities, indicating some known and some new possible communication pathways Our mathematical results confirm important communication pathways that have been discussed in previous research, thus verifying the use of this technique for representing the ribosome, and also reveal new insights into the collective function of ribosomal elements.
Topics: Bacteria; Computational Biology; Gene Regulatory Networks; Protein Biosynthesis; RNA, Ribosomal, 23S; Ribosomal Proteins; Ribosomes; Transcription Elongation, Genetic
PubMed: 33017414
DOI: 10.1371/journal.pone.0239700 -
Trends in Biochemical Sciences Aug 2017The biogenesis of eukaryotic ribosomes is a complicated process during which the transcription, modification, folding, and processing of the rRNA is coupled with the... (Review)
Review
The biogenesis of eukaryotic ribosomes is a complicated process during which the transcription, modification, folding, and processing of the rRNA is coupled with the ordered assembly of ∼80 ribosomal proteins (r-proteins). Ribosome synthesis is catalyzed and coordinated by more than 200 biogenesis factors as the preribosomal subunits acquire maturity on their path from the nucleolus to the cytoplasm. Several biogenesis factors also interconnect the progression of ribosome assembly with quality control of important domains, ensuring that only functional subunits engage in translation. With the recent visualization of several assembly intermediates by cryoelectron microscopy (cryo-EM), a structural view of ribosome assembly begins to emerge. In this review we integrate these first structural insights into an updated overview of the consecutive ribosome assembly steps.
Topics: Cryoelectron Microscopy; Nucleic Acid Conformation; Protein Subunits; Ribosomes
PubMed: 28579196
DOI: 10.1016/j.tibs.2017.05.005 -
Proceedings of the National Academy of... Aug 2020The ribosome translates the genetic code into proteins in all domains of life. Its size and complexity demand long-range interactions that regulate ribosome function....
The ribosome translates the genetic code into proteins in all domains of life. Its size and complexity demand long-range interactions that regulate ribosome function. These interactions are largely unknown. Here, we apply a global coevolution method, statistical coupling analysis (SCA), to identify coevolving residue networks (sectors) within the 23S ribosomal RNA (rRNA) of the large ribosomal subunit. As in proteins, SCA reveals a hierarchical organization of evolutionary constraints with near-independent groups of nucleotides forming physically contiguous networks within the three-dimensional structure. Using a quantitative, continuous-culture-with-deep-sequencing assay, we confirm that the top two SCA-predicted sectors contribute to ribosome function. These sectors map to distinct ribosome activities, and their origins trace to phylogenetic divergences across all domains of life. These findings provide a foundation to map ribosome allostery, explore ribosome biogenesis, and engineer ribosomes for new functions. Despite differences in chemical structure, protein and RNA enzymes appear to share a common internal logic of interaction and assembly.
Topics: Escherichia coli; Evolution, Molecular; Nucleic Acid Conformation; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 23S; Ribosomes
PubMed: 32747536
DOI: 10.1073/pnas.1909634117 -
Trends in Biochemical Sciences May 2019Contrary to the textbook model, recent measurements demonstrated unexpected diversity in ribosomal composition that likely enables specialized translational functions.... (Review)
Review
Contrary to the textbook model, recent measurements demonstrated unexpected diversity in ribosomal composition that likely enables specialized translational functions. Methods based on liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS) enable direct quantification of ribosomal proteins with high specificity, accuracy, and throughput. LC-MS/MS can be 'top-down', analyzing intact proteins, or more commonly 'bottom-up', where proteins are digested to peptides prior to analysis. Changes to rRNA can be examined using either LC-MS/MS or sequencing-based approaches. The regulation of protein synthesis by specialized ribosomes can be examined by multiple methods. These include the popular 'Ribo-Seq' method for analyzing ribosome density on a given mRNA, as well as LC-MS/MS approaches incorporating pulse-labelling with stable isotopes (SILAC) to monitor protein synthesis and degradation.
Topics: Chromatography, Liquid; Models, Molecular; Proteins; RNA, Ribosomal; Ribosomes; Tandem Mass Spectrometry
PubMed: 30792028
DOI: 10.1016/j.tibs.2019.01.008 -
BioMed Research International 2015Although the dynamic motions and peptidyl transferase activity seem to be embedded in the rRNAs, the ribosome contains more than 50 ribosomal proteins (r-proteins),... (Review)
Review
Although the dynamic motions and peptidyl transferase activity seem to be embedded in the rRNAs, the ribosome contains more than 50 ribosomal proteins (r-proteins), whose functions remain largely elusive. Also, the precise forms of some of these r-proteins, as being part of the ribosome, are not structurally solved due to their high flexibility, which hinders the efforts in their functional elucidation. Owing to recent advances in cryo-electron microscopy, single-molecule techniques, and theoretical modeling, much has been learned about the dynamics of these r-proteins. Surprisingly, allosteric regulations have been found in between spatially separated components as distant as those in the opposite sides of the ribosome. Here, we focus on the functional roles and intricate regulations of the mobile L1 and L12 stalks and L9 and S1 proteins. Conformational flexibility also enables versatile functions for r-proteins beyond translation. The arrangement of r-proteins may be under evolutionary pressure that fine-tunes mass distributions for optimal structural dynamics and catalytic activity of the ribosome.
Topics: Allosteric Regulation; Animals; Binding Sites; Catalysis; Computer Simulation; Humans; Models, Biological; Models, Chemical; Models, Molecular; Protein Binding; Protein Conformation; RNA, Ribosomal; Ribosomal Proteins; Ribosomes; Structure-Activity Relationship
PubMed: 26457300
DOI: 10.1155/2015/539238 -
Trends in Biochemical Sciences Jun 2022In addition to their central functions in translation, ribosomes can adopt inactive structures that are fully assembled yet devoid of mRNA. We describe how the abundance... (Review)
Review
In addition to their central functions in translation, ribosomes can adopt inactive structures that are fully assembled yet devoid of mRNA. We describe how the abundance of idle eukaryotic ribosomes is influenced by a broad range of biological conditions spanning viral infection, nutrient deprivation, and developmental cues. Vacant ribosomes may provide a means to exclude ribosomes from translation while also shielding them from degradation, and the variable identity of factors that occlude ribosomes may impart distinct functionality. We propose that regulated changes in the balance of idle and active ribosomes provides a means to fine-tune translation. We provide an overview of idle ribosomes, describe what is known regarding their function, and highlight questions that may clarify their biological roles.
Topics: Polyribosomes; Protein Biosynthesis; RNA, Messenger; Ribosomal Proteins; Ribosomes
PubMed: 35246374
DOI: 10.1016/j.tibs.2022.02.003 -
PloS One 2022Developing mathematical representations of biological systems that can allow predictions is a challenging and important research goal. It is demonstrated here how the...
Developing mathematical representations of biological systems that can allow predictions is a challenging and important research goal. It is demonstrated here how the ribosome, the nano-machine responsible for synthesizing all proteins necessary for cellular life, can be represented as a bipartite network. Ten ribosomal structures from Bacteria and six from Eukarya are explored. Ribosomal networks are found to exhibit unique properties despite variations in the nodes and edges of the different graphs. The ribosome is shown to exhibit very large topological redundancies, demonstrating mathematical resiliency. These results can potentially explain how it can function consistently despite changes in composition and connectivity. Furthermore, this representation can be used to analyze ribosome function within the large machinery of network theory, where the degrees of freedom are the possible interactions, and can be used to provide new insights for translation regulation and therapeutics.
Topics: Ribosomes; Proteins; Bacteria; Eukaryota
PubMed: 36584020
DOI: 10.1371/journal.pone.0279455 -
RNA (New York, N.Y.) May 2019It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal... (Review)
Review
It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.
Topics: Animals; Archaea; Bacteria; Base Sequence; Genetic Heterogeneity; Mammals; Protein Biosynthesis; Protein Processing, Post-Translational; RNA, Messenger; RNA, Transfer; Ribosomal Proteins; Ribosomes; Saccharomyces cerevisiae
PubMed: 30733326
DOI: 10.1261/rna.069823.118 -
Nature Communications Oct 2022The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond...
The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond formation between amino acid substrates is based on entropy trapping, wherein the adjacency of transfer RNA (tRNA)-coupled acyl bonds in the P-site and the α-amino groups in the A-site aligns the substrates for coupling. The plasticity of this catalytic mechanism has been observed in both remnants of the evolution of the genetic code and modern efforts to reprogram the genetic code (e.g., ribosomal incorporation of non-canonical amino acids, ribosomal ester formation). However, the limits of ribosome-mediated polymerization are underexplored. Here, rather than peptide bonds, we demonstrate ribosome-mediated polymerization of pyridazinone bonds via a cyclocondensation reaction between activated γ-keto and α-hydrazino ester monomers. In addition, we demonstrate the ribosome-catalyzed synthesis of peptide-hybrid oligomers composed of multiple sequence-defined alternating pyridazinone linkages. Our results highlight the plasticity of the ribosome's ancient bond-formation mechanism, expand the range of non-canonical polymeric backbones that can be synthesized by the ribosome, and open the door to new applications in synthetic biology.
Topics: Ribosomes; RNA, Transfer; Genetic Code; Peptides; Amino Acids; Protein Biosynthesis
PubMed: 36280685
DOI: 10.1038/s41467-022-33701-2 -
International Journal of Molecular... Apr 2020The synthesis of ribosomes is one of the central and most resource demanding processes in each living cell. As ribosome biogenesis is tightly linked with the regulation... (Review)
Review
The synthesis of ribosomes is one of the central and most resource demanding processes in each living cell. As ribosome biogenesis is tightly linked with the regulation of the cell cycle, perturbation of ribosome formation can trigger severe diseases, including cancer. Eukaryotic ribosome biogenesis starts in the nucleolus with pre-rRNA transcription and the initial assembly steps, continues in the nucleoplasm and is finished in the cytoplasm. From start to end, this process is highly dynamic and finished within few minutes. Despite the tremendous progress made during the last decade, the coordination of the individual maturation steps is hard to unravel by a conventional methodology. In recent years small molecular compounds were identified that specifically block either rDNA transcription or distinct steps within the maturation pathway. As these inhibitors diffuse into the cell rapidly and block their target proteins within seconds, they represent excellent tools to investigate ribosome biogenesis. Here we review how the inhibitors affect ribosome biogenesis and discuss how these effects can be interpreted by taking the complex self-regulatory mechanisms of the pathway into account. With this we want to highlight the potential of low molecular weight inhibitors to approach the dynamic nature of the ribosome biogenesis pathway.
Topics: Animals; Drug Discovery; Gene Expression Regulation; Humans; Molecular Probes; Protein Binding; Protein Biosynthesis; RNA, Ribosomal; Ribosomal Proteins; Ribosomes
PubMed: 32340379
DOI: 10.3390/ijms21082998