Distribution and frequencies of post-transcriptional modifications in tRNAs

Abstract

Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.

Keywords: RNA maturation; comparative analysis; evolution; modified nucleotides; post-transcriptional modification; tRNA; tRNA modifications; tRNA sequence; web server.

Figure 1.

Consensus tRNA secondary structure presented in the “cloverleaf” form with the universal numbering system.

Figure 2.

(A) Distribution of modified residues in tRNA sequences from E. coli as presented by the tRNAmodviz server. Percent of modified residues within each position is mapped onto the consensus tRNA secondary structure (small black and white pie charts within the cloverleaf). (B) Frequency of A, U, C or G bases occurrence and their derivatives in tRNA sequences from E. coli. (C) Color pie charts which present detailed information for chosen position in tRNA sorted by the originating base, sorted by the presence of modification or covering modifications only – these options the user can choose when working with tRNAmodviz.

Figure 3.

Modification profile for tRNA sequences from Gram-negative bacteria (62 sequences from 8 species). The pie charts within each position in the cloverleaf correspond to the percentage of all modified nucleosides (modified being drawn in black). In the tables the series of numbers next to the series of symbols indicate the frequency of occurrence of listed nucleosides at the particular position. The last number corresponds to the frequency of occurrence of the encoded unmodified nucleoside. The numbering of the residues is presented in Figure 1. The list of species from which the analyzed tRNA sequences originate is provided in Supplementary Table.1.

Figure 4.

Modification profile for tRNA sequences from Gram-positive bacteria (72 sequences from 9 species). For the description of the tables and cloverleaf content see the legend for Figure 3. The numbering of the residues is presented in Figure 1. Among sequences considered for this group there are 2 tRNA^Gly isoacceptors from Staphylococcus epidermidis which probably do not function in protein synthesis. These 2 lack the conserved pseudouridine in position 55. The list of species from which the analyzed tRNA sequences originate is provided in Supplementary Table.1.

Figure 5.

Modification profile for tRNA sequences from cytosol of eukaryotic single cell organisms, Fungi and Metazoa (173 sequences from 22 species). For the description of the tables and cloverleaf content see the legend for Figure 3. The numbering of the residues is presented in Figure 1. According to the original work xG37 in 2 R. norvegicus tRNA^Leu was converted to m¹G by treatment with alkali. The list of species from which the analyzed tRNA sequences originate is provided in Supplementary Table.1.

Figure 6.

Modification profile for tRNA sequences from cytosol of Viridiplantae (55 sequences from 14 species). For the description of the tables and cloverleaf content see the legend for Figure 3. The numbering of the residues is presented in Figure 1. xG64 in Scenedesmus obliquus and Triticum aestivum is most probably Gr(p), like in cytoplasmic tRNA^Ini from S. cerevisiae. The list of species from which the analyzed tRNA sequences originate is provided in Supplementary Table.1.

Figure 7.

Modification profile for tRNA sequences from mitochondria (124 sequences from 18 species). For the description of the tables and cloverleaf content see the legend for Figure 3. The numbering of the residues is presented in Figure 1. Note that sequences from Ascaris suum have a lot of deletions and as a result their alignment is problematic. In the majority of cases xA37 is i⁶A37 or ms²i⁶A. In Neurospora crassa tRNA^Tyr m⁵C is present in position e21 or 48. In this compilation m⁵C in e21 and xC48 were kept. The list of species from which the analyzed tRNA sequences originate is provided in Supplementary Table.1.

Figure 8.

Modification profile for tRNA sequences from plastids (38 sequences from 12 species). For the description of the tables and cloverleaf content see the legend for Figure 3. The numbering of the residues is presented in Figure 1. The list of species from which the analyzed tRNA sequences originate is provided in Supplementary Table.1.

Figure 9.

Modification profile for tRNA sequences from Euryarchaeota (60 sequences, mostly Haloferax volcanii). For the description of the tables and cloverleaf content see the legend for Figure 3. The numbering of the residues is presented in Figure 1. xA57 present in initiator tRNA from Thermoplasma acidophilum is not m¹I. The list of species, from which the analyzed tRNA sequences originate, is provided in Supplementary Table.1.

Figure 10.

Frequency of modification marked on the structure of yeast tRNA^Phe (PDB ID: 1ehz). The color scale from blue via white to red indicates the percentage in which each position is modified when all sequenced tRNAs are considered. The arrow indicates the interface of interactions between the D- and TΨ-loops.