Post-transcriptional nucleotide modification and alternative folding of RNA

Abstract

Alternative foldings are an inherent property of RNA and a ubiquitous problem in scientific investigations. To a living organism, alternative foldings can be a blessing or a problem, and so nature has found both, ways to harness this property and ways to avoid the drawbacks. A simple and effective method employed by nature to avoid unwanted folding is the modulation of conformation space through post-transcriptional base modification. Modified nucleotides occur in almost all classes of natural RNAs in great chemical diversity. There are about 100 different base modifications known, which may perform a plethora of functions. The presumably most ancient and simple nucleotide modifications, such as methylations and uridine isomerization, are able to perform structural tasks on the most basic level, namely by blocking or reinforcing single base-pairs or even single hydrogen bonds in RNA. In this paper, functional, genomic and structural evidence on cases of folding space alteration by post-transcriptional modifications in native RNA are reviewed.

Figure 1

Anticodon stem loops (ASLs) of well studied classical tRNAs. (A) Yeast tRNA^Phe including m¹G37, the natural precursor of the hypermodified wybutosine base found at position 37 of the fully matured native tRNA (compare Figure 2). (B) E.coli tRNA^Phe ASL modification isoforms. The unmodified ASL displays (left) a hairpin structure with a small loop of three nucleotides and two extra base pairs U32-A38 and U33-A37. Introduction of i⁶A as sole nucleotide modification leads two the formation of the classical ASL-stem loop structure including a U-turn (middle). An ASL corresponding to that of the native tRNA^Phe would include Ψ32, Ψ39 and ms²i⁶A modification (right). (C) tRNA^Lys(NUU) from E.coli contains mnms²U (x = m) and t6A, while the tRNA from human cytosol contains mcms²U (x = c) and ms2t6A.The human mitochondrial tRNA^Lys has a similar stem and an identical loop sequence (compare Figure 5) and contains τm⁵U (x = τ).

Figure 2

(A) Secondary structure of yeast tRNA^Phe. Modified nucleotides are in bold. Tertiary interactions are indicated by dotted lines. (B) General architecture of classical elongator tRNAs. On the cloverleaf structure on the left, conserved residues important for elements of tertiary structure are indicated. R stands for conserved purine residues and Y stands for conserved pyrimidine residues. Frequently modified positions [>25%; according to reference (121)] in the anticodon are highlighted by circles. Frequently modified positions elsewhere in the tRNA are boxed. Tertiary interactions are indicated by dotted lines. In the representation on the right, acceptor and anticodon domains are arranged in an L-shape according to the 3D structure. (C) Reinforcement hypothesis. On the left, the unmodified tRNA forms a stable acceptor domain and a loosely structured anticodon domain (weak interactions are symbolized by grey dotted lines). Class I modification enzymes act on the acceptor domain and introduce modifications like T54, Ψ55, m¹A58, m⁵C48, m⁵C49 and/or others, as indicated by arrows. These modifications stabilize the T-loop structure and reinforce tertiary interactions with the D-loop. The formerly loose structure of the anticodon domain is thus better defined (symbolized by black lines) and now allows better substrate recognition by other modification enzymes.

Figure 3

Slight deviations from the classical tRNA structure. (A) Secondary structure of initiator ${\text{tRNA}}_{\text{I}}^{\text{Met}}$ from yeast. Modified nucleotides are in bold. Tertiary interactions are indicated by dotted lines. Note the absence of T54 and Ψ55 and the additional tertiary interactions between the A20 and the T-loop as compared to tRNA^Phe. R denotes a purine at position 59 of ${\text{tRNA}}_{\text{I}}^{\text{Met}}$ for which sequence data in the literature are contradictory (96,89). (B) Human mitochondrial tRNA^Leu(UUR). The secondary structure of the native tRNA including all modified bases is shown on the left. Modified nucleotides are in bold and tertiary interactions are indicated by dotted lines. The loose structure of the anticodon domain of the unmodified transcript (98) is shown on the right. Modified nucleotides are abbreviated according to references (96,122).

Figure 4

Rearrangements on the secondary structure level induced by double methylation of human cytosolic tRNA^Asn. The calculated structure of the unmodified transcript on the left side features an aberrant D-stem without G10, but including G26. Double methylation on N6 of G26 impedes its Watson–Crick pairing with cytidines and thus renders the base pair G26-C11, which is highlighted by a box, impossible. The fully modified tRNA^Asn may thus adopt the classical cloverleaf structure as shown on the right. U? denotes an unknown modified uridine, likely a derivative of ribothymidine, at position 54.

Figure 5

Methylation-induced rearrangement of human mitochondrial tRNA^Lys. (A) Cloverleaf secondary structure of the fully modified human mitochondrial tRNA^Lys. (B) The extended hairpin secondary structure of the unmodified transcript of human mitochondrial tRNA^Lys (left) is converted to the cloverleaf by methylation on N1-A9, as evidenced in a chimeric tRNA containing m¹A9 as single modified nucleotide (right). The methylation prevents an A9-U64 base pair (boxed) in the extended hairpin structure on the left. Modified nucleotides in bold are abbreviated according to references (96,122).

Figure 6

Possible influence of a conserved methylation pattern in rRNA. An unmodified oligoribonucleotide derived from helix 45 of a bacterial small subunit rRNA shows two alternative conformations in equilibrium, with K around 3, favouring the structure shown on the upper right. Introduction of several methyl groups restricts conformation space and results in the equilibrium being shifted almost completely to the structure shown on the lower left. Modified nucleotides are abbreviated according to reference (24).