The multiple flavors of GoU pairs in RNA

Westhof, Éric; Yusupov, Marat; Yusupova, G.

doi:10.1002/jmr.2782

Cited by 30 publications

(38 citation statements)

References 77 publications

(163 reference statements)

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“…2a, Supplementary Figure S1). While it is often assumed that the T (or U) base primarily moves to form a wobble (Westhof et al 2019;Westhof 2014), the structures show both bases move to form the wobble pair as noted previously for G•T mismatches in A-DNA (Rabinovich et al 1988) (Fig. 2b).…”

Section: Wobble G•t Mismatches Have a Distinct Sugar-backbone Conformsupporting

confidence: 67%

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

et al. 2020

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NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.

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Section: Wobble G•t Mismatches Have a Distinct Sugar-backbone Conformsupporting

confidence: 67%

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

et al. 2020

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“…The combination of a sulfur atom in position 2 and an electron-withdrawing or electron-donating side chain in position 5 promotes various tautomeric forms of uracil, i.e., a 2,4-diketo form (K in Figure 7A,B), an E4 tautomer ( Figure 7C), or a zwitterionic ZI form ( Figure 7D). This "chameleon" ability explains how R5S2U hybridizes with an A complement (the K form) and a G complement (K, E4, or ZI forms) [44]. The latter modes (E4 and ZI) were previously demonstrated in the crystal structures of mcm5S2U 34 -tRNA (U E4 -G) and mnm5S2U-tRNA (U ZI -G) bound to mRNA models accommodated at the ribosome [41,43], and were confirmed by physicochemical and theoretical studies [45].…”

Section: Discussionsupporting

confidence: 52%

“…In contrast to the above results of thermodynamic measurements, biological experiments demonstrated that synonymous mRNA codons with 3 -A-and 3 -G-ending units are equally well recognized by tRNAs with anticodons containing wobble modified uridines, especially those containing sulfur at position 2 and bearing specific substituents at position 5 [20,38,39]. Recent data suggested that in a biological context (e.g., tRNA bound to mRNA at the ribosome), modified uridine 34 units (U* 34 ) can recognize guanosine units by at least two different hydrogen bonding patterns, depending on the substituents at positions 2 and 5 of the uracil ring [40][41][42][43][44][45]. While U* 34 -G base-pairing data are available for 5-substituted uridines and 2-thiouridines, data for corresponding 5-substituted 2-selenouridines identified in tRNAs are limited [46,47].…”

Section: Introductionmentioning

confidence: 99%

C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons

Leszczyńska

Cypryk

Gostyński

et al. 2020

IJMS

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5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1-3 were assessed to be significantly lower compared to their 2-thio-and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called "new wobble base pair", which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5 -NNG-3 synonymous codons, unlike their 2-thio-and 2-oxo-precursors, which preferentially read the 5 -NNA-3 codons. Thus, the interplay between the levels of U-, S2U-and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3 -A-and 3 -G-ending codons.

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“…Modification of U34 is necessary for decoding G3 ending codons. The modification in U34 (U34*) changes the chemical structure of the U34 so that a pair U34*-G3, with the U displaced into the minor groove, and not into the major groove, can be stabilized (Rozov et al 2016;Westhof et al 2019). Several U34containing tRNAs were observed modified either at position C5 and/or at position C2.…”

Section: Modifications At Position 34 (Table 2)mentioning

confidence: 99%

Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea

Wolff

Villette

Zumsteg

et al. 2020

RNA

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To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius. Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.

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The multiple flavors of GoU pairs in RNA

Cited by 30 publications

References 77 publications

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons

Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea

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