Fig 1.
Secondary structure of tRNASec and tRNASer.
Cloverleaf models of tRNASec (A–C) and of a canonical tRNA (tRNASer, D) in Homo sapiens (A and D, eukaryota), Methanococcus maripaludis (B, archaea) and Escherichia coli (C, bacteria). The acceptor arm, D arm, anticodon arm, variable arm and T arm are colored red, yellow, green, blue and purple, respectively. The anticodon triplet UCA (complementary to the UGA codon) is indicated with circled residues. The position 73, known as the discriminator base, is the fourth residue from the 3’ end, and is also circled. tRNASec structures (A–C) were obtained with Secmarker. The tRNASer structure (D) was obtained from tRNAdb 2009 [42]. The 3’ terminal CCA triplet is usually encoded in the genome in bacteria, while it is added post-transcriptionally in archaea and eukaryotes. The tRNASec plots are examples of the graphical output of Secmarker.
Table 1.
Performance statistics of tRNASec prediction for the three programs tested.
Fig 2.
tRNASec predictions in eukaryotic genomes.
(A) Phylogenetic tree of the eukaryotic genomes used in the benchmark set. Sec-containing species are drawn in bold font. The tRNASec predictions are indicated with dots. The size of each dot is proportional to the number of predictions. Open dots indicate a single prediction. The color of the cells indicate the outcome of the test, for each program. Species marked with a star (*) are discussed in the Results section and/or S1 Text. The approximate species phylogeny was obtained from the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy). Figure produced using our R package ggsunburst, available at http://genome.crg.es/∼dsantesmasses/ggsunburst. (B) Venn diagram showing the overlap between the tRNASec genes predicted by the three programs. Numbers in black correspond to predictions in Sec-containing genomes. Purple numbers correspond to predictions in Sec-devoid genomes.
Fig 3.
tRNASec predictions in bacterial genomes.
(A) Phylogenetic tree of the bacterial genomes used in the benchmark set. Sec-containing species are drawn in bold font. Genome names were cut down to species level (not including the strain) for visualization purposes. The complete names including strain identifiers are provided in S1 Table. Species marked with a star (*) are discussed in the Results section and/or S1 Text. (B) Venn diagram showing the overlap between the tRNASec genes predicted by the three programs. See Fig 2 caption for details.
Fig 4.
tRNASec predictions in archaea genomes.
(A) Phylogenetic tree of the archaeal genomes used in the benchmark set. Sec-containing species are drawn in bold font. Genome names were cut down to species level (not including the strain) for visualization purposes. The complete names including strain identifiers are provided in S1 Table. (B) Venn diagram showing the overlap between the tRNASec genes predicted by the three programs. See Fig 2 caption for details.
Table 2.
Total number of genomes analyzed and tRNASec predictions by Secmarker.
Fig 5.
The discriminator base G73 in tRNASec.
Sequence logos [53] of the 3’ end of tRNASec candidates from the three domains of life. The subsequences include the AT-stem, starting at position 61 of tRNA (numbering based on [35]) and extends further into the 3’ region of the gene. The residue in position 73 (the discriminator base) shows a strongly conserved G (guanine). (A) 9/4 fold tRNA cloverleaf structure indicating the 13 base pairs acceptor plus T-arm sequence used in the logos. (B) Bacteria, 2316 sequences; (C) archaea, 20 sequences; (D) eukaryota, 562 sequences; (E) bacterial 7/5 fold tRNASec candidates, including 47 sequences with a shorter 12 bp AT-stem. tRNAs have a poly-T motif in the 3’ region as the transcription termination signal [54], here only visible in archaea because of the low number of sequences. Only the top scoring candidate in each genome were used to generate the logos.
Fig 6.
Duplication of tRNASec in hominids.
Pol III binding in human tRNASec1 (A) and tRNASec2 (B) by Chip-seq (tracks ERR039133 and ERR039141, see Materials and Methods). Conserved syntenic genes surrounding tRNASec1 (C) and tRNASec2 (D) in the genome of five hominids. tRNASec1 is flanked by the genes FOSB and RTN2, and tRNASec2 is located within an intron of PARVB. (E) Structural alignment of tRNASec1 in eleven primates (top) and tRNASec2, only found in hominids (bottom). Panels A and B were produced with the UCSC genome browser [60] on the human hg19 assembly. “100 Vert. Cons” track corresponds to sequence conservation across 100 vertebrates. Protein coding annotations in panels C and D were obtained with Selenoprofiles [24]. Sequences in panel E were obtained with Secmarker, aligned using Infernal (cmalign program) [31], and visualized with RALEE [61]. RALEE highlights the nucleotides that are paired according to the consensus secondary structure at the bottom of the alignment, and that also respect the standard pairing rules. The rightmost column in the alignment corresponds to the discriminator base.
Table 3.
Species with multiple tRNASec candidates.
Fig 7.
“Redox-active disulfide protein 2” selenoproteins in Brachyspira.
(A) Multiple sequence alignment containing amino acid sequences obtained from UniRef90 (top four) and from Brachyspira genomes using Selenoprofiles [24]. In the Brachyspira sequences, the Sec position (column 26) is coloured according to the codon found in the genome: Cys in red; and Sec in green. The thioredoxin domain spans from column 53 to the C-terminus. (B) Genomic arrangement of the three “Redox-active disulfide protein 2” genes, all of them found in a gene cluster in each of the Brachyspira genomes (rows). The genes are coloured according to the codon in the Sec position (marked in black), following the same colouring scheme as panel A. Selenoproteins were either missed or truncated in the annotations provided by NCBI, here represented in darker color and labeled with the NCBI gene name. No annotation was found in NCBI for B. innocent and B. hyodysenteriae. All genes are represented 5’ to 3’; the scale measures nucleotides and is centered on the start codon of the “Sec.1” gene. (C) Structure alignments of the putative SECIS found downstream the TGA codon (underlined in red) in the two selenoproteins, “Sec.1” (left) and “Sec.2” (right). Alignments produced using Infernal [31] and visualized with RALEE [61]. See Fig 6 for RALEE colouring scheme.
Fig 8.
Structure conservation of tRNASec across eukaryotes.
Arc diagram of eukaryotic tRNASec displaying covariation information. The arcs link the residues that form each pair in the tRNA secondary structure, and are colored according to the covariation (top legend). The blocks correspond to the structural alignment of the tRNASec sequences, and are colored according to the covariation in each sequence (bottom legend). The labels on the right indicate the name of the species, which are clustered by their phylogeny (left panel). Plot produced with R-chie [69]. In R-chie the covariation values (top legend) have a range of [-2, 2], where -2 is a complete lack of pairing potential and sequence conservation, 0 is complete sequence conservation regardless of pairing potential, and 2 is a complete lack of sequence conservation but maintaining pairing.
Fig 9.
Two snapshots showing the input form (left) and the output page (right). The results shown correspond to the two human tRNASec.