Translation: The Universal Structural Core of Life

Bernier, Chad R.; Petrov, Anton S.; Kovacs, Nicholas A.; Penev, Petar I.; Williams, Loren Dean

doi:10.1093/molbev/msy101

Cited by 70 publications

(128 citation statements)

References 60 publications

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“…The SEREB MSA [30] was used as a seed to align additional eukaryotic es3 sequences. The SSU rRNA sequences in the SEREB MSA were used to search [31] the NCBI databases [32] for SSU rRNA sequences.…”

Section: Phylogeny and Multiple Sequence Alignmentsmentioning

confidence: 99%

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

et al. 2019

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Mammalian and bird ribosomes are nearly twice the mass of prokaryotic ribosomes in part because of their extraordinarily long rRNA tentacles. Human rRNA tentacles are not fully observable in current three-dimensional structures and their conformations remain to be fully resolved. In previous work we identified sequences that favor G-quadruplexes in silico and in vitro in rRNA tentacles of the human large ribosomal subunit. We demonstrated by experiment that these sequences form G-quadruplexes in vitro. Here, using a more recent motif definition, we report additional G-quadruplex sequences on surfaces of both subunits of the human ribosome. The revised sequence definition reveals expansive arrays of potential G-quadruplex sequences on LSU tentacles. In addition, we demonstrate by a variety of experimental methods that fragments of the small subunit rRNA form G-quadruplexes in vitro. Prior to this report rRNA sequences that form G-quadruplexes were confined to the large ribosomal subunit. Our combined results indicate that the surface of the assembled human ribosome contains numerous sequences capable of forming G-quadruplexes on both ribosomal subunits. The data suggest conversion between duplexes and G-quadruplexes in response to association with proteins, ions, or other RNAs. In some systems it seems likely that the integrated population of RNA G-quadruplexes may be dominated by rRNA, which is the most abundant cellular RNA.

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Section: Phylogeny and Multiple Sequence Alignmentsmentioning

confidence: 99%

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

et al. 2019

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“…The ribosome is responsible for the synthesis of all coded proteins and contains life’s most conserved ribonucleic acids. The common core of the ribosome is universal to all life (1,2) and has been essentially invariant since the last universal common ancestor (3-5). Thus, ribosomes can be interrogated as molecular fossils (6-8).…”

Section: Introductionmentioning

confidence: 99%

Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage

Guth-Metzler

Bray

Frenkel-Pinter

et al. 2019

Preprint

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5Divalent metal cations are essential to the structure and function of the ribosome. Previous 2 6 characterizations of ribosome structure and function performed under standard laboratory 2 7conditions have implicated Mg 2+ as the primary mediator of ribosomal structure and function. 8The contribution of Fe 2+ as a ribosomal cofactor has been largely overlooked, despite the 2 9 ribosome's evolution in a high Fe 2+ environment, and its continued use by obligate anaerobes 3 0 inhabiting high Fe 2+ niches. Here we show that (i) iron readily cleaves RNA by a non-oxidative 3 1 mechanism that has not been detected previously, (ii) functional ribosomes purified from cells 3 2 grown under low O 2 , high Fe 2+ conditions are associated with Fe 2+ , (iii) a small subset of Fe 2+ 3 3that is associated with the ribosome is not exchangeable with surrounding cations, presumably 3 4 because they are highly coordinated by rRNA. In total, these results expand the ancient role of 3 5 iron in biochemistry, suggest a novel method for regulation of translation by iron, and highlight a 3 6 possible new mechanism of iron toxicity. 3 7

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“…The translation system, which synthesizes all coded protein (6, 7), originated and matured during the Archean Eon (4-2.5 Ga) in low-O 2 , high-Fe 2+ , and high-Mn 2+ conditions (8). The common core of the ribosome, and many other aspects of the translation system, have remained essentially frozen since the last universal common ancestor (9). In extant biochemistry, Mg 2+ ions are essential for both structure and function of the ribosome (10) and other enzymes involved in translation (11).…”

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confidence: 99%

Multiple prebiotic metals mediate translation

Bray

Lenz

Haynes

et al. 2018

Preprint

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15In extant biochemistry, Mg 2+ ions are essential for both structure and function of the ribosome (4,5) and for 16functions of many enzymes involved in translation (6). The translation system, which synthesizes all coded 17 protein (7), originated and matured during the Archean Eon (4-2.5 Ga; (8)). The common core of the 18 ribosome and many other aspects of the translation system have remained essentially frozen since the last 19 universal common ancestor (9,10). 20In ribosomes, structural Mg 2+ ions occur in rRNA-Mg 2+ clamps (11) (Fig. 1a), in dinuclear Mg 2+ -21 microclusters that frame the peptidyl transferase center (12) (Fig. 1b), and at the SSU-LSU interface (13) 22( Fig. 1c). Functional Mg 2+ ions stabilize a critical bend in mRNA between the P-site and A-site codons (14) 23 (Fig. 1d), and mediate rRNA-tRNA/mRNA interactions (15) (Fig. 1e, f 26All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. 97RO). Thus, a total of 2.5 mM "background" Mg 2+ was present in each reaction (Fig. S1) MgCl2 and FeCl2 which were tested over a range of final concentrations (1, 3, 4, 5, 6, 7, 8, 9, and 11 mM; 122 All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. the amounts of metals in our assay reaction, which had no effect on DHFR activity (data not shown). 136Ribosome iron content. In order to measure the iron content of ribosomes, a 300 µL reaction was prepared 137 containing 45 µL of a 13.3 µM stock of E. coli ribosomes (New England Biolabs catalog # P0763S), 7 mM

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Translation: The Universal Structural Core of Life

Cited by 70 publications

References 60 publications

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage

Multiple prebiotic metals mediate translation

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