Escherichia coli tRNA 2‐selenouridine synthase (SelU) converts S2U‐RNA to Se2U‐RNA via S‐geranylated‐intermediate

Abstract

To date the only tRNAs containing nucleosides modified with a selenium (5-carboxymethylaminomethyl-2-selenouridine and 5-methylaminomethyl-2-selenouridine) have been found in bacteria. By using tRNA anticodon-stem-loop fragments containing S2U, Se2U, or geS2U, we found that in vitro tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA in a two-step process involving S2U-RNA geranylation (with ppGe) and subsequent selenation of the resulting geS2U-RNA (with SePO ). No 'direct' S2U-RNA→Se2U-RNA replacement is observed in the presence of SelU/SePO only (without ppGe). These results suggest that the in vivo S2U→Se2U and S2U→geS2U transformations in tRNA, so far claimed to be the elementary reactions occurring independently in the same domain of the SelU enzyme, should be considered a combination of two consecutive events - geranylation (S2U→geS2U) and selenation (geS2U→Se2U).

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

“…Electrostatic potential energy maps illustrating the charge distributions in the mnm5Se2U base analyzed by quantum chemical calculations were drawn up for three the most stable tautomeric forms of the m1mnm5Se2Ura model, i.e., K, E4, and E2, protonated at the amino alkyl residue; these are shown in Figure S31. The data presented for tautomers of m1mnm5Se2Ura were similar to those presented for m1mnm5S2Ura and m1mnm5Ura [25], demonstrating that in the zwitterionic tautomeric structure, the electron-deficient region is located in the vicinity of the ammonium cation at the side chain, while the electron-rich region is dispersed over the Se2 . .…”

“…As noted recently, tRNA 2-selenouridine synthase SelU, i.e., the enzyme responsible for S→Se replacement, also catalyzes the S-geranylation of 2-thiouridine in tRNAs. Contrary to earlier suggestions, it was recently demonstrated that S-geranylated tRNA primarily acts as the intermediate in S2U-tRNA→Se2U-tRNA transformation [24,25] and does not seem to serve as an amino acid carrier at the ribosome or bind to bacterial cell membranes [21,23,26].…”

“…90%, Table 2, data given in brackets; Since R5S2Us offer at least four hybridization options, two questions arise: (1) Why did Nature develop a complex enzymatic system in bacteria (SelU, SelD, and the enzymes involved in synthesis of the geranyl component) which converts the corresponding thio-precursors 5 and 6 into 2-Se-modifications 1 and 2 in the iso-acceptor tRNAs decoding synonymous 5 -NNA-3 and 5 -NNG-3 codons? (2) What are the functions of R5S2Us, which are "safely" disabled due to this conversion that is apparently elicited ad hoc [25]? To have the tools necessary to answer these questions, we synthesized Se2-uridines 1-3 and compared their physicochemical and structural properties to the S2-uridine precursors 5-7, as well to the uridine parent units 8-10.…”

“…Currently, the most effective strategy of 2-selenium incorporation relies on S-alkylation (S-methylation or S-geranylation) of sugar-protected 2-thiouridine, followed by thioalkyl→SeH substitution with sodium hydrogen selenide (NaSeH) [24,29,30]. Consequently, effective synthesis of a phosphoramidite derivative of suitably protected Se2U was developed, and numerous synthetic Se2U-RNAs were obtained for structural, physicochemical and functional studies [25,29,30]. Huang and co-workers, who pioneered the chemical synthesis of various Se-derivatives of nucleic acids [31], also developed enzymatic synthesis of Se2U-RNAs utilizing 2-selenouridine triphosphate (Se2UTP) and RNA transcription [32].…”

Recent Advances in Our Understanding of the Biosynthesis of Sulfur Modifications in tRNAs

“…se 2 U34 is synthesized from s 2 U34 via geranylated intermediate (ges 2 U) by SelU (YbbB) ( Chen et al, 2005 ; Dumelin et al, 2012 ; Sierant et al, 2018b ). Desulfuration activity of 2-thiouracil by DUF523 domain protein in the cell has recently been reported ( Aucynaite et al, 2018 ).…”