Transfer RNA Modification: Presence, Synthesis, and Function

Abstract

Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.

Distribution and frequencies of post-transcriptional modifications in tRNAs

“…Modified residues of the third class are found at unique positions of only a limited group of tRNA species and the corresponding modification enzymes are, as expected, very diverse and often species-specific. 10 The distribution of modified residues in tRNAs of different groups of organisms was examined several decades ago. [11][12][13] The previous compilations demonstrated notable differences in the modification patterns of tRNA originating from organisms distantly related in evolution, the diversity of modifications was noted especially at position 34 and conserved purine at position 37 of anticodon (reviewed in ref.…”

A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes

“…These results suggest that the diverse tRNA thiolation processes in archaea and eukaryotic cytosols share a common mechanism dependent on a [3Fe-4S] cluster for sulfur transfer. U nucleoside is found at position 8 of most bacterial and archaeal tRNAs and functions as a photosensor for near-UV irradiation (1). Upon irradiation, the s 4 U8 cross-links with the nearby cytidine at position 13.…”

“…Upon irradiation, the s 4 U8 cross-links with the nearby cytidine at position 13. This reaction causes conformational changes and prevents aminoacylation of tRNAs, resulting in accumulations of uncharged tRNAs that trigger stringent responses (1) U acts as an identity element in aminoacylation reactions (5-7), promotes tRNA binding to the ribosomal A-site (7), and prevents frameshifting during translation (8). Yeast mutants lacking the 2-thio modification have pleotropic phenotypes, such as defects in invasive growth (9), hypersensitivity to high temperature, rapamycin, caffeine, or oxidative stress (10,11), inability to maintain normal metabolic cycles (12), and protein misfolding and aggregation (13).…”

Celebrating wobble decoding: Half a century and still much is new

“…39 It may affect translational efficiency of rare codons that are intrinsically inefficient in decoding. 19,135 The s 2 C 32 modification has also been found in archaeal tRNA. 136 Pseudouridine, Ψ, although present at the anticodon wobble position 34, is another modification found predominantly at positions 32, 38 and 39.…”

“…The s 2 C 32 modification is present in E. coli and Salmonella enterica tRNA Arg ICG which decodes CGU/C and CGA in the absence of s 2 C 32 , tRNA Arg CCG that decodes CGG, tRNA Arg with the modified anticodon mnm 5 UCU that decodes AGA/G, and tRNA Ser GCU decoding AGC/U. 19,39 The presence of s 2 C 32 negates I 34 wobbling to A3. 39 It may affect translational efficiency of rare codons that are intrinsically inefficient in decoding.…”