Anionic G•U pairs in bacterial ribosomal rRNAs

Abstract

Wobble GU pairs (or G•U) occur frequently within double-stranded RNA helices interspersed between standard G=C and A-U Watson-Crick pairs. Another type of G•U pair interacting via their Watson-Crick edges has been observed in the A site of ribosome structures between a modified U34 in the tRNA anticodon triplet and G+3 in the mRNA. In such pairs the electronic structure of the U is changed with a negative charge on N3(U), resulting in two H-bonds between N1(G)…O4(U) and N2(G)…N3(U). Here, we report that such pairs occur in other highly conserved positions in ribosomal RNAs of bacteria in the absence of U modification. An anionic cis Watson-Crick G•G pair is also observed and well conserved in the small subunit. These pairs are observed in tightly folded regions.

NMR measurements of transient low-populated tautomeric and anionic Watson–Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing

“…The second ES had chemical shifts (Δω G-N1 = 1 ± 7 ppm and Δω U-N3 = 58 ± 7 ppm) consistent with an anionic Watson–Crick-like dG·rU − with population p ES = 0.12 ± 0.06% and exchange rate k ex = 5000 ± 2000 s −1 . The 15 N chemical shifts as well as other lines of evidence ( 8 , 77 , 78 ) rule out an anionic inverted wobble conformation which has been reported in some crystal structures of DNA polymerase ( 38 , 79 ), in complexes of the ribosome, mRNA and modified tRNA ( 80 , 81 ), as well as in ribosomal RNA ( 82 ). Furthermore, the anionic and tautomeric species exchange with k ex,minor = 13000 ± 6000 s −1 (Figure 2B ).…”

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg2+

“…Next, we describe a few peculiarities of the 8B0X structure. According to a recent study (66), four anionic base pairs are present in 8B0X and in bacterial ribosomes in general. Two in the SSU and one in the LSU are related to U(-)•G pairs ( Figure 12 ).…”