Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland

Abstract

Nature combines existing biochemical building blocks, at times with subtlety of purpose. RNA modifications are a prime example of this, where standard RNA nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. The result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. Here, we highlight several modifications that, because of their chemical intricacy, rely on seemingly unrelated pathways to provide cofactors for their synthesis. Besides their immediate role in affecting RNA function, modifications may act as sensors and transducers of information that connect a cell's metabolic state to its translational output, carefully orchestrating a delicate balance between metabolic rate and protein synthesis at a system's level.

Figure 1. Selected Modified Ribonucleosides

(A) Adenosine modifications resulting from conjugation to ubiquitous electrophilic metabolites. (B) Chemically sophisticated hypermodifications discovered throughout the past five decades. The year of publication is given in brackets. (C) C5-modified cytidines related to so call epigenetic DNA modifications recently discovered. m⁶A, 6-methyladenosine; ac⁶A, 6-acetyladenosine; t⁶A, 6-threonyladenosine; i⁶A, 6-isopentenyladenosine; Arp, 2’-O-ribosyladenosine phosphate; yW, wybutosine; oQ, epoxyqueuosine; tm⁵U, 5-taurinomethyluridine; nm⁵ges²U, 5-aminomethyl-2-geranyluridine; 5-methyluridine; ho⁵C, 5-hydroxycytidine; f⁵C, 5-formyluridine.

Figure 2. Hypermodification Pathways

(A) Eukaryotic modification network of uridines at the wobble position 34. The weave results from the overlay of independently operating modification pathways, which modify at positions 2’-O of the ribose, C5 of the uridines, or O₂ of the uridines. The lack of a fixed order of action generates a multitude of permutations. (B) Biosynthesis pathway of wybutosine derivatives. Note that transformations occur in a defined serial manner. Since branching pathways do not reunite, the pathway by which a given modification is generated is unambiguous. Numbers in parentheses refer to the TYW1-5 enzymes involved in each step and referred to in the main text. Question marks (?) indicate reactions for which the given enzyme is not known.

Figure 2. Hypermodification Pathways

(A) Eukaryotic modification network of uridines at the wobble position 34. The weave results from the overlay of independently operating modification pathways, which modify at positions 2’-O of the ribose, C5 of the uridines, or O₂ of the uridines. The lack of a fixed order of action generates a multitude of permutations. (B) Biosynthesis pathway of wybutosine derivatives. Note that transformations occur in a defined serial manner. Since branching pathways do not reunite, the pathway by which a given modification is generated is unambiguous. Numbers in parentheses refer to the TYW1-5 enzymes involved in each step and referred to in the main text. Question marks (?) indicate reactions for which the given enzyme is not known.

Figure 3. Chemical Strategies for C5 Modification of Uridines in Bacteria

The C5 position of uridines is rendered nucleophilic by Michael addition of a cysteine thiolate to the 5,6 double bond. 5,10-methylene tetrahydrofolate (5,10-CH₂THF) provides a C1-body at the oxidation state of formaldehyde which acts as electrophile (red), leading to an electrophilic 5-methyleneuridine intermediate. This intermediate can be attacked by a variety of nucleophiles (blue), which may include hydride (from THF), or different aminoacids such as glycine (bacteria) or taurine (metazoan mitochondria). After dealkylation of cmnm⁵U, the resulting 5-aminomethyluridine (nm⁵U) can be methylated to mnm⁵U or prenylated to inm⁵U. The latter reaction is unconfirmed.

Figure 4. Hypermodifications at Positions 34 and 37 in the Anticodon Loop

Positions 34 and 37 of the anticodon loop undergo by far the largest diversity of post-transcriptional modifications. Highlighted are modified uridines (upper left panel) and guanosines (lower left panel); ubiquitous hypermodifications ensuring correct decoding at the wobble position. Sophisticated purine modifications found at position 37 (upper and lower right panels) play roles in reading frame maintenance.

Figure 5. Various Metabolic Pathways Contribute Co-factors for Modification

The figure shows hyper-modifications highlighted in this review that require building blocks from common metabolic pathways. For example, pyruvate derived from glycolysis. These interconnections may suggest coupling between metabolic and translational rates. The individual color boxes correspond to those modifications shown in figure 4.