Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA

Abstract

In contrast to GNRA tetraloop receptors that are common in RNA, receptors for the more thermostable UNCG loops have remained elusive for almost three decades. An analysis of all RNA structures with resolution ≤3.0 Å from the PDB allowed us to identify three previously unnoticed receptors for UNCG and GNRA tetraloops that adopt a common UNCG fold, named ‘Z-turn’ in agreement with our previously published nomenclature. These receptors recognize the solvent accessible second Z-turn nucleotide in different but specific ways. Two receptors participating in a complex network of tertiary interactions are associated with the rRNA UUCG and GAAA Z-turns capping helices H62 and H35a in rRNA large subunits. Structural comparison of fully assembled ribosomes and comparative sequence analysis of >6500 rRNA sequences helped us recognize that these motifs are almost universally conserved in rRNA, where they may contribute to organize the large subunit around the subdomain-IV four-way junction. The third UCCG receptor was identified in a rRNA/protein construct crystallized at acidic pH. These three non-redundant Z-turn receptors are relevant for our understanding of the assembly of rRNA and other long-non-coding RNAs, as well as for the design of novel folding motifs for synthetic biology.

Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome

“…Besides 2x_bulge modules, many other loop/receptor interactions are likely metastable when the receptors and/or loops are in their unbound state. This has been observed for the T-loop (72), Z-turn loop motifs (73), GAAA/11nt interaction (21,25) and several other loop/receptor interactions isolated by SELEX such as R1 (24). Moreover, sub-optimality in terms of folding and assembly has been noticed for other recurrent RNA modules identified in the ribosome.…”

“…Like L39/H89, they can require additional RNA elements, ribosomal proteins or post-transcriptional modifications for efficient folding and assembly in their natural context. RNA metastability plays an important role for RNA remodeling during the regulated and controlled maturation of the ribosome (17,73–75). As a matter of fact, the intrinsic ability of RNA to form metastable structures is at the root of many remarkable functions of RNA, including riboswitches (76).…”

Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding

“…The junctional loop J1 (residing between P1 and P1a) zippers up and forms a long-distance interaction with J2 (residing between stems P1a and P1b) (Figure 1C – F and Supplementary Figure S2B ). NAD + is bound at the intersection of stem P1 and the junction loop J1, employing a type-I A minor base triple ( 27 , 28 ).…”

Z-DNA and Z-RNA in human disease

“…In a separate study, a left-handed quadruplex with a syn-anti dinucleotide step was described 28 . Another motif with a Z-like dinucleotide syn-anti conformation, called a Z-turn, was found in RNA junctions, ribosome−protein interactions 29 , the CUG splicing protein 30 and the IFIT5 RNA protein complex 31 . So far, none of the interactions have been base-specific.…”