Origin and Evolution of the Ribosome

Fox, George E.

doi:10.1101/cshperspect.a003483

Cited by 216 publications

(212 citation statements)

References 126 publications

(128 reference statements)

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“…The ribosome in its present form was well-established at the emergence of the last universal common ancestor of life (LUCA) (Woese 2001;Wolf and Koonin 2007;Smith et al 2008;Bokov and Steinberg 2009;Belousoff et al 2010;Fox 2010). There is a consensus that some parts of the ribosome are even older than LUCA, predating the protein world.…”

Section: Evolutionary Implications Of the Domain Structure Of The Dommentioning

confidence: 99%

“…The ribosome is our most direct macromolecular connection to the distant evolutionary past and to early life (Woese 2001;Wolf and Koonin 2007;Smith et al 2008;Bokov and Steinberg 2009;Belousoff et al 2010;Fox 2010). The ribosome is believed to have emerged from the ''RNA world '' (Rich 1962;Woese 1967;Crick 1968;Orgel 1968;Gilbert 1986) following an evolutionary pathway that preserved ribosomal RNAs as central players in peptide bond formation and decoding (Noller et al 1992;Ban et al 2000;Nissen et al 2000;Harms et al 2001;Ogle et al 2001;Yusupov et al 2001;Schuwirth et al 2005;Selmer et al 2006).…”

Section: Introductionmentioning

confidence: 99%

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Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Athavale¹,

Gossett²,

Hsiao³

et al. 2012

RNA

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The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter-and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 29-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.

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Section: Evolutionary Implications Of the Domain Structure Of The Dommentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Athavale¹,

Gossett²,

Hsiao³

et al. 2012

RNA

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“…Ribosomal DNA (rDNA) encoding rRNA, with its roots descending from the RNA world, is the most ancient part of all known genomes on the Earth, which provides unique insights into the origins of genome architecture, as well as metabolic features of life at the root of the evolutionary tree [1]. To date, however, rRNA-determining sequences and the associated chromatin remain 'dark matter' of eukaryotic genomes due to their exceptionally excessive and repetitive nature, hindering efficient characterization and experimentation.…”

Section: Introductionmentioning

confidence: 99%

Nucleolar dominance and maternal control of 45S rDNA expression

et al. 2015

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Using a system of interspecies hybrids, trihybrids, and recombinants with varying proportions of genomes from three distinct Xenopus species, we provide evidence for de novo epigenetic silencing of paternal 45S ribosomal ribonucleic acid (rRNA) genes and their species-dependent expression dominance that escapes transcriptional inactivation after homologous recombination. The same pattern of imprinting is maintained in the offspring from mothers being genetic males (ZZ) sex-reversed to females, indicating that maternal control of ribosomal deoxyribonucleic acid (rDNA) expression is not sex-chromosome linked. Nucleolar dominance (nucleolus underdevelopment) in Xenopus hybrids appears to be associated with a major non-Mendelian reduction in the number of 45S rDNA gene copies rather than a specific pattern of their expression. The loss of rRNA gene copies in F 1 hybrids was non-random with respect to the parental species, with the transcriptionally dominant variant preferentially removed from hybrid zygotes. This dramatic disruption in the structure and function of 45S rDNA impacts transcriptome patterns of small nucleolar RNAs and messenger RNAs, with genes from the ribosome and oxidative stress pathways being among the most affected. Unorthodoxies of rDNA inheritance and expression may be interpreted as hallmarks of genetic conflicts between parental genomes, as well as defensive epigenetic mechanisms employed to restore genome integrity.

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“…In both cases the rRNA expansion serves as a scaffold for the addition of new proteins. Such progressive expansion shares principles with the development of modern ribosomes themselves from primordial ancestors (25). In addition to these changes at the surface, there is a substantial remodeling of the tunnel through which the nascent protein chain proceeds as it emerges from the ribosome.…”

Section: Overall Structurementioning

confidence: 98%

The Structure of the Yeast Mitochondrial Large Ribosomal Subunit

Brown¹,

Amunts²,

Bai³

et al. 2014

Acta Cryst Sect A

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# These authors contributed equally to this work. AbstractMitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using singleparticle electron cryo-microscopy. The resolution of 3.2 Ångstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site and a putative membrane docking site.Mitochondria are organelles in eukaryotic cells that play a major role in metabolism, especially the synthesis of ATP. During evolution, mitochondria have lost or transferred most of their genes to the nuclei, significantly reducing the size of their genome (1). In yeast, all but one of the few remaining protein genes encode subunits of respiratory chain complexes, whose synthesis involves insertion into the inner mitochondrial membrane along with incorporation of prosthetic groups (2). For the translation of these genes, mitochondria maintain their own ribosomes (mitoribosomes) and translation system. The mitochondrial ribosomal RNA and several tRNAs are encoded by the mitochondrial genome, whereas all but one of its ribosomal proteins are nuclear encoded and imported from the cytoplasm. Mitoribosomes have diverged greatly from their counterparts in the cytosol of bacterial and eukaryotic cells and also exhibit high variability depending on species (Table S1) (3). Several genetic diseases map to mitoribosomes (4). In addition, the toxicity of many ribosomal antibiotics, in particular aminoglycosides, is thought to be due to their interaction with the mitoribosome (5).Mitochondrial translation in the yeast Saccharomyces cerevisiae (6) has been used as a model to study human mitochondrial diseases (7). The 74S yeast mitoribosome has an overall molecular weight of 3 MDa, or 30% higher than that of their bacterial counterpart. It consists of a 54S large subunit (1.9 MDa) and a 37S small subunit (1.1 MDa). Highresolution crystal structures have been solved for bacterial (8, 9) and eukaryotic ribosomes (10-12), as well as for an archaeal large subunit (13). In comparison, the only structures to † To whom correspondence should be addressed at scheres@mrc-lmb.cam.ac.uk or ramak@mrc-lmb.cam.ac.uk. Europe PMC Funders Group Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts date for mitoribosomes come from electron cryo-microscopy (cryo-EM) reconstructions at 12-14 Å (14-16).The very low yields of mitoribosomes from most tissues have impeded their crystallization. However, the advent of high-speed direct electron detectors (that allow accounting for particle movement during imaging) (17, 18), and improved algorithms for the classification and alignment of particles (19), allowed us to determine the structure of the large subunit of the yeast mitoribosome (hereafter referred t...

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Origin and Evolution of the Ribosome

Cited by 216 publications

References 126 publications

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Nucleolar dominance and maternal control of 45S rDNA expression

The Structure of the Yeast Mitochondrial Large Ribosomal Subunit

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