RNA modifying enzymes shape tRNA biogenesis and function

Abstract

Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning to emerge. tRNAs have two general clusters of modifications. The first cluster is within the anticodon stem-loop including several modifications essential for protein translation. The second cluster of modifications is within the tRNA elbow, and roles for these modifications are less clear. In general, tRNA elbow modifications are typically not essential for cell growth, but nonetheless several tRNA elbow modifications have been highly conserved throughout all domains of life. In addition to forming modifications, many tRNA modifying enzymes have been demonstrated or hypothesized to also play an important role in folding tRNA acting as tRNA chaperones. In this review, we summarize the known functions of tRNA modifying enzymes throughout the lifecycle of a tRNA molecule, from transcription to degradation. Thereby, we describe how tRNA modification and folding by tRNA modifying enzymes enhance tRNA maturation, tRNA aminoacylation, and tRNA function during protein synthesis, ultimately impacting cellular phenotypes and disease.

Keywords: RNA; RNA binding protein; RNA folding; RNA methylation; RNA modification; RNA processing; RNA structure; aminoacyl tRNA synthetase; precursor tRNA (pre-tRNA); protein synthesis; ribosome; transfer RNA (tRNA).

Figure 1

tRNA structure and modification.A, cloverleaf secondary structure (left) and L-shaped tertiary structure (right) typical of the majority of tRNAs. B, locations and identities of all modifications in Escherichia coli tRNAs. Common modifications are denoted by color, as indicated in the legend, which also indicates the abbreviations for these common modifications. Modifications are systematically abbreviated with letters preceding the nucleotide indicating a base modification. Superscript numbers indicate the position of the nucleotide where the modification is found. Letters after the nucleotide indicate modification to the ribose sugar. More explanation for the abbreviation of tRNA modifications is excellently summarized in (1). Multiple different modifications can occur at positions 32, 34, and 37 in different tRNAs, as shown in tables. Abbreviations not included in the legend but present in the table are as follows: acp–aminocarboxypropyl, I–inosine, ac–acetyl, k–lysidine, (c)mnm–(carboxy)methylaminomethyl, Se–selenium, Q–queuosine, ho–hydroxy, cmo–carboxymethoxy, mcmo–methoxycarbonylmethoxy, i–isopentyl, (c)t–(cyclic)threonylcarbamoyl. C, locations of modifications within the E. coli tRNA^Phe structure (82) as a typical tRNA to demonstrate clusters of modifications in the tRNA elbow and in the tRNA anticodon stem-loop. Modifications are colored as per the legend in panel B. D, examples of some of the modifications found within tRNAs. Atoms that constitute each modification are indicated in red.

Figure 2

General lifecycle of a tRNA. Following transcription of pre-tRNA by RNA polymerase (1), tRNA undergoes several maturation steps (2) including 5ʹ and 3ʹ end processing, intron splicing, modification of many nucleotides, and RNA folding, giving rise to a mature tRNA. Mature tRNA is then aminoacylated to form aminoacyl-tRNA (aa-tRNA), which binds EF-Tu•GTP, forming the ternary complex for delivery to the ribosome (3). Various ribonucleases target tRNA to degrade aberrantly matured tRNA (4) or to cleave tRNA into functional tRNA-derived small RNAs (tDR) (5). Finally, tRNAs also participate in a variety of nontranslation alternative processes (6).

Figure 3

Examples of tRNA-protein complex structures illustrating the various interactions of tRNAs throughout its lifecycle. In all cases, tRNA is colored black and is in roughly the same orientation to demonstrate how different proteins interact with various surfaces of the tRNA. From left to right on the top row: yeast unbound tRNA (PDB: 4TNA) (237); Pyrococcus horikoshii ArcTGT homodimer colored in shades of red bound to two tRNA^Val molecules to modify G15 with tRNA adopting the lambda form. The second tRNA molecule is shown in gray (1J2B) (89); Archaeoglobus fulgidus TiaS bound to tRNA^Ile2 for modifying C34 (PDB: 3AMT) (238); Escherichia coli RlmN bound to tRNA^Glu for modification of A37 (PDB: 5HR7) (239); E. coli DusC bound to tRNA^Trp to modify U16 (PDB ID: 4YCP) (240) and Thermus thermophilus Dus bound to tRNA^Phe to modify U20 (PDB: 3B0V) (241) displaying how different dihydrouridine synthases target different tRNA residues. The second line contains the METTL1 (dark blue) and WDR4 (light blue) heterodimer bound to tRNA to modify G46 (PDB: 8EG0) (242); Thermus aquaticus EF-Tu bound to tRNA^Cys (PDB: 1B23) (243); yeast AspRS bound to tRNA (PDB: 1ASZ) (244); human mitochondrial protein only RNase P in complex with pre-tRNA^Tyr. RNase P is colored in dark blue, TRMT10C is colored in light blue, and MRPP3 is colored in indigo (PDB: 7ONU) (43); and Thermotoga maritima RNase P in complex with tRNA^Phe (PDB: 3Q1Q) (245). The protein component is colored in pink and the RNA in gray. PDB, Protein Data Bank.

Figure 4

Summary of the roles of modifications during different steps of translation.A, tRNA modifying enzymes whose absence in vivo affects global translation, specific codon translation, or frameshifting. Model organism used in each study is indicated in parenthesis. Hs: Homo sapiens, Tt: Thermus thermophilus, Pa: Pseudomonas aeruginosa, Ec: Escherichia coli, Sc: Saccharomyces cerevisiae, St: Salmonella typhimurium, mito: mitochondria. B, general schematic of the overall steps of translation. Modifications found to play roles within each step are highlighted within colored boxes.