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

Abstract

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.

Different Oxidation Pathways of 2-Selenouracil and 2-Thiouracil, Natural Components of Transfer RNA

“…This result allowed them to conclude that selenium-containing biomolecules are resistant to permanent oxidation, and this is the main reason for naturally occurring selenium in both 2-selenouridine- and Sec-containing proteins. This conclusion complementary to the latest data on the role of seleno modifications in tRNA ensuring the fidelity of the reading of synonymous 3′-G ending codons [ 19 ], prompted us to perform more detailed studies on the oxidation of 2-thiouracil (S2Ura) and 2-selenouracil (Se2Ura), especially in light of the recently discovered “oxidative desulfuration” of S2U, leading predominantly to 4-pyrimidinone derivatives [ 13 , 14 , 15 , 16 , 17 ].…”

Selenium‐NMR Spectroscopy in Organic Synthesis: From Structural Characterization Toward New Investigations

“…[108] In 2020, Nawrot and co-workers described the synthesis of 5-methylaminomethyl-2-selenouridines and the study of their properties toward base pairing with guanosine. [109] Based on pH-dependent potentiometric titration, pKa values for the N3H groups of the synthetized selenouridines and their functional role were assessed. It was observed that in the physiological conditions, these compounds adopted preferentially the zwitterionic form.…”

2-Selenouridine, a Modified Nucleoside of Bacterial tRNAs, Its Reactivity in the Presence of Oxidizing and Reducing Reagents

“…Selenol/diselenide exchange reactions were evidenced by the fact that, under the conditions used, i.e., in phosphate buffer with a pH of 7.4, about half of the selone 1 was deionized (p K a 7.30 [ 26 ]) and formed the selenolate anion I ( Figure 4 a). In the next step, the positively charged diselenide II reacted with selenolate I, forming the neutral form of diselenide 2 by exchange process (equilibrium reactions).…”

“…The observed chemical shift and line broadening were probably due to the deprotonation of selenol Se2U to selenolate form at pH 7.4, as its p K a was 7.30 and ca. was 50% in ionized form, in contrast to more acidic conditions [ 26 , 53 , 54 ]. Moreover, we can conclude that the exchange process between selenol/diselenide depends more on the buffer pH than on the temperature, as shown by the 77 Se NMR studies in water and at pH 7.4.…”

“…However, why nature evolved this novel enzymatic process and introduced selenium into the wobble uridines of tRNA is not yet known. The recent literature reports on the physicochemical properties of sulfur- and selenium-containing uridines suggest that R5Se2U34, similar to R5S2U34, may play a role in regulating the translation process by modulating codon-anticodon recognition and reading off the synonymous codons NNG-3′ and NNA-3′ within mRNA [ 25 , 26 ]. This is a particularly interesting problem in the bacterial system, where a single tRNA Lys reads both AAA -3′ and AAG-3′ codons, while a single tRNA Glu accepts the GAA-3′ and GAG -3′ codons [ 8 , 12 , 27 , 28 ].…”