Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Structure, Function and Evolution of the Ribosome

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 April 2019) | Viewed by 94621

Share This Special Issue

Special Issue Editors

Prof. Dr. Zachary F Burton

E-Mail Website
Guest Editor

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA

Prof. Dr. Robert Root-Bernstein

E-Mail Website
Guest Editor

Department of Physiology, Michigan State University, East Lansing, MI, USA
Interests: prebiotic chemical ecology; origins of life; origins of genetic code; origins of homochirality; molecular complementarity; origins of cellular transporters and receptors; STEM education; scientific creativity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The ribosome is one of only four structures known to occur in the cells of all organisms (the others being membranes, chromosomes, and acidocalcisomes). While a great deal of research has been devoted to the origins and evolution of the genetic basis of life, much less has been focused on the origins and evolution of ribosomal structure and function. Without more such studies, we cannot understand the intricate ways in which transcription and translation emerged in the first living organisms and then shaped, and were shaped by, their subsequent evolution. Recent advances in ribosome studies suggest that the time is ripe for investigators to pool their efforts, ideas and data on the ways that ribosome structure and function originated and evolved.

Papers are requested on the subject of the structure, function and evolution of the ribosome. The editors are particularly interested in the following topics:

What was the form and function of the first ribosomes?
How did the peptidyl transferase center evolve?
How did aminoacyl-tRNA synthetase class I and class II enzymes evolve?
How did the genetic code evolve?
How important is dehydration to the function of the peptidyl transferase center?
How central was tRNA evolution to evolution of the ribosome?
How essential was tRNA, ribosome and genetic code evolution for the evolution of cellular life?
What are the ribosome functions associated with tRNA wobble base recognition?
What are the essential features of the decoding center of the ribosome? Did this evolve separately from the peptidyl transferase center or in tandem?
What are mechanisms of ribosome proofreading of tRNA-mRNA interactions?
How is the transition from a polymer, minihelix and/or RNA-dominated world to a cloverleaf tRNA world accomplished?
What roles did ribozymes play in ribosome evolution?
How can artificial intelligence and novel proteonomic methods be applied to studies of the ribosome, aminoacyl-tRNA synthetase enzymes, tRNA and the genetic code?
How did viruses evolve to co-opt ribosome functions?
Did viruses shape ribosome evolution?

Keywords

ribosome
evolution
structure
function
transcription
translation
regulation
transfer RNA
ribosomal RNA
ribosomal proteins
peptidyl transferase center
tRNA synthetase
proofreading
ribozymes
genetic code
prebiotic
virus

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (14 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

25 pages, 6071 KiB

Open AccessArticle

Migration of Small Ribosomal Subunits on the 5′ Untranslated Regions of Capped Messenger RNA

by Nikolay E. Shirokikh, Yulia S. Dutikova, Maria A. Staroverova, Ross D. Hannan and Thomas Preiss

Int. J. Mol. Sci. 2019, 20(18), 4464; https://doi.org/10.3390/ijms20184464 - 10 Sep 2019

Cited by 13 | Viewed by 4206

Abstract

Several control mechanisms of eukaryotic gene expression target the initiation step of mRNA translation. The canonical translation initiation pathway begins with cap-dependent attachment of the small ribosomal subunit (SSU) to the messenger ribonucleic acid (mRNA) followed by an energy-dependent, sequential ‘scanning’ of the 5′ untranslated regions (UTRs). Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase eukaryotic initiation factor (eIF) 4A and its efficiency contributes to the specific rate of protein synthesis. Thus, understanding the molecular details of the scanning mechanism remains a priority task for the field. Here, we studied the effects of inhibiting ATP-dependent translation and eIF4A in cell-free translation and reconstituted initiation reactions programmed with capped mRNAs featuring different 5′UTRs. An aptamer that blocks eIF4A in an inactive state away from mRNA inhibited translation of capped mRNA with the moderately structured β-globin sequences in the 5′UTR but not that of an mRNA with a poly(A) sequence as the 5′UTR. By contrast, the nonhydrolysable ATP analogue β,γ-imidoadenosine 5′-triphosphate (AMP-PNP) inhibited translation irrespective of the 5′UTR sequence, suggesting that complexes that contain ATP-binding proteins in their ATP-bound form can obstruct and/or actively block progression of ribosome recruitment and/or scanning on mRNA. Further, using primer extension inhibition to locate SSUs on mRNA (‘toeprinting’), we identify an SSU complex which inhibits primer extension approximately eight nucleotides upstream from the usual toeprinting stop generated by SSUs positioned over the start codon. This ‘−8 nt toeprint’ was seen with mRNA 5′UTRs of different length, sequence and structure potential. Importantly, the ‘−8 nt toeprint’ was strongly stimulated by the presence of the cap on the mRNA, as well as the presence of eIFs 4F, 4A/4B and ATP, implying active scanning. We assembled cell-free translation reactions with capped mRNA featuring an extended 5′UTR and used cycloheximide to arrest elongating ribosomes at the start codon. Impeding scanning through the 5′UTR in this system with elevated magnesium and AMP-PNP (similar to the toeprinting conditions), we visualised assemblies consisting of several SSUs together with one full ribosome by electron microscopy, suggesting direct detection of scanning intermediates. Collectively, our data provide additional biochemical, molecular and physical evidence to underpin the scanning model of translation initiation in eukaryotes. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

23 pages, 5951 KiB

Open AccessArticle

A tRNA-mimic Strategy to Explore the Role of G34 of tRNA^Gly in Translation and Codon Frameshifting

by Aurélie Janvier, Laurence Despons, Laure Schaeffer, Antonin Tidu, Franck Martin and Gilbert Eriani

Int. J. Mol. Sci. 2019, 20(16), 3911; https://doi.org/10.3390/ijms20163911 - 11 Aug 2019

Cited by 2 | Viewed by 4146

Abstract

Decoding of the 61 sense codons of the genetic code requires a variable number of tRNAs that establish codon-anticodon interactions. Thanks to the wobble base pairing at the third codon position, less than 61 different tRNA isoacceptors are needed to decode the whole set of codons. On the tRNA, a subtle distribution of nucleoside modifications shapes the anticodon loop structure and participates to accurate decoding and reading frame maintenance. Interestingly, although the 61 anticodons should exist in tRNAs, a strict absence of some tRNAs decoders is found in several codon families. For instance, in Eukaryotes, G34-containing tRNAs translating 3-, 4- and 6-codon boxes are absent. This includes tRNA specific for Ala, Arg, Ile, Leu, Pro, Ser, Thr, and Val. tRNA^Gly is the only exception for which in the three kingdoms, a G34-containing tRNA exists to decode C3 and U3-ending codons. To understand why G34-tRNA^Gly exists, we analysed at the genome wide level the codon distribution in codon +1 relative to the four GGN Gly codons. When considering codon GGU, a bias was found towards an unusual high usage of codons starting with a G whatever the amino acid at +1 codon. It is expected that GGU codons are decoded by G34-containing tRNA^Gly, decoding also GGC codons. Translation studies revealed that the presence of a G at the first position of the downstream codon reduces the +1 frameshift by stabilizing the G34•U3 wobble interaction. This result partially explains why G34-containing tRNA^Gly exists in Eukaryotes whereas all the other G34-containing tRNAs for multiple codon boxes are absent. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

15 pages, 4408 KiB

Open AccessArticle

Co-Assembly of 40S and 60S Ribosomal Proteins in Early Steps of Eukaryotic Ribosome Assembly

by Jesse M. Fox, Rebekah L. Rashford and Lasse Lindahl

Int. J. Mol. Sci. 2019, 20(11), 2806; https://doi.org/10.3390/ijms20112806 - 8 Jun 2019

Cited by 3 | Viewed by 4897

Abstract

In eukaryotes three of the four ribosomal RNA (rRNA) molecules are transcribed as a long precursor that is processed into mature rRNAs concurrently with the assembly of ribosomal subunits. However, the relative timing of association of ribosomal proteins with the ribosomal precursor particles and the cleavage of the precursor rRNA into the subunit-specific moieties is not known. To address this question, we searched for ribosomal precursors containing components from both subunits. Particles containing specific ribosomal proteins were targeted by inducing synthesis of epitope-tagged ribosomal proteins followed by pull-down with antibodies targeting the tagged protein. By identifying other ribosomal proteins and internal rRNA transcribed spacers (ITS1 and ITS2) in the immuno-purified ribosomal particles, we showed that eS7/S7 and uL4/L4 bind to nascent ribosomes prior to the separation of 40S and 60S specific segments, while uS4/S9, uL22, and eL13/L13 are bound after, or simultaneously with, the separation. Thus, the incorporation of ribosomal proteins from the two subunits begins as a co-assembly with a single rRNA molecule, but is finished as an assembly onto separate precursors for the two subunits. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

34 pages, 2809 KiB

Open AccessArticle

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

by Robert Root-Bernstein and Meredith Root-Bernstein

Int. J. Mol. Sci. 2019, 20(1), 140; https://doi.org/10.3390/ijms20010140 - 2 Jan 2019

Cited by 21 | Viewed by 6851

Abstract

We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Graphical abstract

12 pages, 2358 KiB

Open AccessArticle

Muller’s Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia

by Sergey V. Melnikov, Kasidet Manakongtreecheep, Keith D. Rivera, Arthur Makarenko, Darryl J. Pappin and Dieter Söll

Int. J. Mol. Sci. 2018, 19(12), 4125; https://doi.org/10.3390/ijms19124125 - 19 Dec 2018

Cited by 20 | Viewed by 6397

Abstract

Microsporidia are fungi-like parasites that have the smallest known eukaryotic genome, and for that reason they are used as a model to study the phenomenon of genome decay in parasitic forms of life. Similar to other intracellular parasites that reproduce asexually in an environment with alleviated natural selection, Microsporidia experience continuous genome decay that is driven by Muller’s ratchet—an evolutionary process of irreversible accumulation of deleterious mutations that lead to gene loss and the miniaturization of cellular components. Particularly, Microsporidia have remarkably small ribosomes in which the rRNA is reduced to the minimal enzymatic core. In this study, we analyzed microsporidian ribosomes to study an apparent impact of Muller’s ratchet on structure of RNA and protein molecules in parasitic forms of life. Through mass spectrometry of microsporidian proteome and analysis of microsporidian genomes, we found that massive rRNA reduction in microsporidian ribosomes appears to annihilate the binding sites for ribosomal proteins eL8, eL27, and eS31, suggesting that these proteins are no longer bound to the ribosome in microsporidian species. We then provided an evidence that protein eS31 is retained in Microsporidia due to its non-ribosomal function in ubiquitin biogenesis. Our study illustrates that, while Microsporidia carry the same set of ribosomal proteins as non-parasitic eukaryotes, some ribosomal proteins are no longer participating in protein synthesis in Microsporidia and they are preserved from genome decay by having extra-ribosomal functions. More generally, our study shows that many components of parasitic cells, which are identified by automated annotation of pathogenic genomes, may lack part of their biological functions due to continuous genome decay. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

13 pages, 2365 KiB

Open AccessArticle

Hypothesis: Spontaneous Advent of the Prebiotic Translation System via the Accumulation of L-Shaped RNA Elements

by Ilana Agmon

Int. J. Mol. Sci. 2018, 19(12), 4021; https://doi.org/10.3390/ijms19124021 - 12 Dec 2018

Cited by 6 | Viewed by 3426

Abstract

The feasibility of self-assembly of a translation system from prebiotic random RNA chains is a question that is central to the ability to conceive life emerging by natural processes. The spontaneous materialization of a translation system would have required the autonomous formation of proto-transfer RNA (tRNA) and proto-ribosome molecules that are indispensable for translating an RNA chain into a polypeptide. Currently, the vestiges of a non-coded proto-ribosome, which could have only catalyzed the formation of a peptide bond between random amino acids, is consensually localized in the region encircling the peptidyl transferase center of the ribosomal large subunit. The work presented here suggests, based on high resolution structures of ribosomes complexed with messenger RNA (mRNA) and tRNAs, that three types of L-shaped RNA building blocks derived from the modern ribosome, alongside with an L-shaped proto-tRNA, each composed of about 70-mer, could have randomly occurred in the prebiotic world and combined to form a simple translation system. The model of the initial coded proto-ribosome, which includes the active sites of both ribosomal subunits, together with a bridging element, incorporates less than 6% of the current prokaryotic rRNA, yet it integrates all of the ribosomal components that are vital for synthesizing the earliest coded polypeptides. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Graphical abstract

15 pages, 3307 KiB

Open AccessArticle

Type-II tRNAs and Evolution of Translation Systems and the Genetic Code

by Yunsoo Kim, Bruce Kowiatek, Kristopher Opron and Zachary F. Burton

Int. J. Mol. Sci. 2018, 19(10), 3275; https://doi.org/10.3390/ijms19103275 - 22 Oct 2018

Cited by 18 | Viewed by 5096

Abstract

Because tRNA is the core biological intellectual property that was necessary to evolve translation systems, tRNAomes, ribosomes, aminoacyl-tRNA synthetases, and the genetic code, the evolution of tRNA is the core story in evolution of life on earth. We have previously described the evolution of type-I tRNAs. Here, we use the same model to describe the evolution of type-II tRNAs, with expanded V loops. The models are strongly supported by inspection of typical tRNA diagrams, measuring lengths of V loop expansions, and analyzing the homology of V loop sequences to tRNA acceptor stems. Models for tRNA evolution provide a pathway for the inanimate-to-animate transition and for the evolution of translation systems, the genetic code, and cellular life. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Graphical abstract

Review

Jump to: Research

37 pages, 3126 KiB

Open AccessReview

Control of Translation at the Initiation Phase During Glucose Starvation in Yeast

by Yoshika Janapala, Thomas Preiss and Nikolay E. Shirokikh

Int. J. Mol. Sci. 2019, 20(16), 4043; https://doi.org/10.3390/ijms20164043 - 19 Aug 2019

Cited by 20 | Viewed by 8673

Abstract

Glucose is one of the most important sources of carbon across all life. Glucose starvation is a key stress relevant to all eukaryotic cells. Glucose starvation responses have important implications in diseases, such as diabetes and cancer. In yeast, glucose starvation causes rapid and dramatic effects on the synthesis of proteins (mRNA translation). Response to glucose deficiency targets the initiation phase of translation by different mechanisms and with diverse dynamics. Concomitantly, translationally repressed mRNAs and components of the protein synthesis machinery may enter a variety of cytoplasmic foci, which also form with variable kinetics and may store or degrade mRNA. Much progress has been made in understanding these processes in the last decade, including with the use of high-throughput/omics methods of RNA and RNA:protein detection. This review dissects the current knowledge of yeast reactions to glucose starvation systematized by the stage of translation initiation, with the focus on rapid responses. We provide parallels to mechanisms found in higher eukaryotes, such as metazoans, for the most critical responses, and point out major remaining gaps in knowledge and possible future directions of research on translational responses to glucose starvation. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

12 pages, 500 KiB

Open AccessReview

Proteomic Techniques to Examine Neuronal Translational Dynamics

by Shon A. Koren, Drew A. Gillett, Simon V. D’Alton, Matthew J. Hamm and Jose F. Abisambra

Int. J. Mol. Sci. 2019, 20(14), 3524; https://doi.org/10.3390/ijms20143524 - 18 Jul 2019

Cited by 11 | Viewed by 5620

Abstract

Impairments in translation have been increasingly implicated in the pathogenesis and progression of multiple neurodegenerative diseases. Assessing the spatiotemporal dynamics of translation in the context of disease is a major challenge. Recent developments in proteomic analyses have enabled the resolution of nascent peptides in a short timescale on the order of minutes. In addition, a quantitative analysis of translation has progressed in vivo, showing remarkable potential for coupling these techniques with cognitive and behavioral outcomes. Here, we review these modern approaches to measure changes in translation and ribosomal function with a specific focus on current applications in the mammalian brain and in the study of neurodegenerative diseases. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

22 pages, 34010 KiB

Open AccessReview

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

by Youri Timsit and Daniel Bennequin

Int. J. Mol. Sci. 2019, 20(12), 2911; https://doi.org/10.3390/ijms20122911 - 14 Jun 2019

Cited by 10 | Viewed by 3659

Abstract

In the past few decades, studies on translation have converged towards the metaphor of a “ribosome nanomachine”; they also revealed intriguing ribosome properties challenging this view. Many studies have shown that to perform an accurate protein synthesis in a fluctuating cellular environment, ribosomes sense, transfer information and even make decisions. This complex “behaviour” that goes far beyond the skills of a simple mechanical machine has suggested that the ribosomal protein networks could play a role equivalent to nervous circuits at a molecular scale to enable information transfer and processing during translation. We analyse here the significance of this analogy and establish a preliminary link between two fields: ribosome structure-function studies and the analysis of information processing systems. This cross-disciplinary analysis opens new perspectives about the mechanisms of information transfer and processing in ribosomes and may provide new conceptual frameworks for the understanding of the behaviours of unicellular organisms. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

47 pages, 2219 KiB

Open AccessReview

Signal Transduction in Ribosome Biogenesis: A Recipe to Avoid Disaster

by Manuela Piazzi, Alberto Bavelloni, Angela Gallo, Irene Faenza and William L. Blalock

Int. J. Mol. Sci. 2019, 20(11), 2718; https://doi.org/10.3390/ijms20112718 - 3 Jun 2019

Cited by 56 | Viewed by 10407

Abstract

Energetically speaking, ribosome biogenesis is by far the most costly process of the cell and, therefore, must be highly regulated in order to avoid unnecessary energy expenditure. Not only must ribosomal RNA (rRNA) synthesis, ribosomal protein (RP) transcription, translation, and nuclear import, as well as ribosome assembly, be tightly controlled, these events must be coordinated with other cellular events, such as cell division and differentiation. In addition, ribosome biogenesis must respond rapidly to environmental cues mediated by internal and cell surface receptors, or stress (oxidative stress, DNA damage, amino acid depletion, etc.). This review examines some of the well-studied pathways known to control ribosome biogenesis (PI3K-AKT-mTOR, RB-p53, MYC) and how they may interact with some of the less well studied pathways (eIF2α kinase and RNA editing/splicing) in higher eukaryotes to regulate ribosome biogenesis, assembly, and protein translation in a dynamic manner. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Graphical abstract

14 pages, 1723 KiB

Open AccessReview

Two Old Dogs, One New Trick: A Review of RNA Polymerase and Ribosome Interactions during Transcription-Translation Coupling

by Adam B. Conn, Stephen Diggs, Timothy K. Tam and Gregor M. Blaha

Int. J. Mol. Sci. 2019, 20(10), 2595; https://doi.org/10.3390/ijms20102595 - 27 May 2019

Cited by 16 | Viewed by 7736

Abstract

The coupling of transcription and translation is more than mere translation of an mRNA that is still being transcribed. The discovery of physical interactions between RNA polymerase and ribosomes has spurred renewed interest into this long-standing paradigm of bacterial molecular biology. Here, we provide a concise presentation of recent insights gained from super-resolution microscopy, biochemical, and structural work, including cryo-EM studies. Based on the presented data, we put forward a dynamic model for the interaction between RNA polymerase and ribosomes, in which the interactions are repeatedly formed and broken. Furthermore, we propose that long intervening nascent RNA will loop out and away during the forming the interactions between the RNA polymerase and ribosomes. By comparing the effect of the direct interactions between RNA polymerase and ribosomes with those that transcription factors NusG and RfaH mediate, we submit that two distinct modes of coupling exist: Factor-free and factor-mediated coupling. Finally, we provide a possible framework for transcription-translation coupling and elude to some open questions in the field. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

24 pages, 1984 KiB

Open AccessReview

The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways

by A. Maxwell Burroughs and L Aravind

Int. J. Mol. Sci. 2019, 20(8), 1981; https://doi.org/10.3390/ijms20081981 - 23 Apr 2019

Cited by 34 | Viewed by 5912

Abstract

The evolution of release factors catalyzing the hydrolysis of the final peptidyl-tRNA bond and the release of the polypeptide from the ribosome has been a longstanding paradox. While the components of the translation apparatus are generally well-conserved across extant life, structurally unrelated release factor peptidyl hydrolases (RF-PHs) emerged in the stems of the bacterial and archaeo-eukaryotic lineages. We analyze the diversification of RF-PH domains within the broader evolutionary framework of the translation apparatus. Thus, we reconstruct the possible state of translation termination in the Last Universal Common Ancestor with possible tRNA-like terminators. Further, evolutionary trajectories of the several auxiliary release factors in ribosome quality control (RQC) and rescue pathways point to multiple independent solutions to this problem and frequent transfers between superkingdoms including the recently characterized ArfT, which is more widely distributed across life than previously appreciated. The eukaryotic RQC system was pieced together from components with disparate provenance, which include the long-sought-after Vms1/ANKZF1 RF-PH of bacterial origin. We also uncover an under-appreciated evolutionary driver of innovation in rescue pathways: effectors deployed in biological conflicts that target the ribosome. At least three rescue pathways (centered on the prfH/RFH, baeRF-1, and C12orf65 RF-PH domains), were likely innovated in response to such conflicts. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Figure 1

25 pages, 8070 KiB

Open AccessReview

Ribosome Structure, Function, and Early Evolution

by Kristopher Opron and Zachary F. Burton

Int. J. Mol. Sci. 2019, 20(1), 40; https://doi.org/10.3390/ijms20010040 - 21 Dec 2018

Cited by 32 | Viewed by 15849

Abstract

Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel motion between the head/beak and the body of the 30S subunit was observed. A tilting dynamic of the head/beak versus the body of the 30S subunit was detected using simulations. A reversible ratcheting motion was seen between the 30S and the 50S subunits that slide relative to one another. The 30S–50S intersubunit contacts regulate translocation. IF2, EF-Tu, and EF-G are homologous G-protein GTPases that cycle on and off the same site on the ribosome. The ribosome, aminoacyl-tRNA synthetase (aaRS) enzymes, transfer ribonucleic acid (tRNA), and messenger ribonucleic acid (mRNA) form the core of information processing in cells and are coevolved. Surprisingly, class I and class II aaRS enzymes, with distinct and incompatible folds, are homologs. Divergence of class I and class II aaRS enzymes and coevolution of the genetic code are described by analysis of ancient archaeal species. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of the Ribosome)

► Show Figures

Journal Menu

Journal Browser

Structure, Function and Evolution of the Ribosome

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (14 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI