tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features

Abstract

From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria.

tRNAHis maturation: An essential yeast protein catalyzes addition of a guanine nucleotide to the 5′ end of tRNAHis

“…1A;Sprinzl et al 1998;Marck and Grosjean 2002). In prokaryotes, this G −1 residue is genome-encoded, and originates from anomalous RNase P cleavage of the precursor tRNA His (pre-tRNA His ) at the −1 position to generate tRNA with an additional G −1 :C 73 base pair in the acceptor stem (Orellana et al 1986;Burkard et al 1988).…”

Initiator tRNA Genes Template the 3’CCA End at High Frequencies in Bacteria

“…Critically, because the C1-A72 mismatch motif of tRNA fMet is known to compromise the efficiency of processing at the 5′-end [23], we suggest that direct transcription of the CCA sequence can serve as a determinant to help with 5'-end processing [24,25]. In contrast, initiator tRNAs in Archaea have WatsonCrick base-pairs in the 1-72 position [21] so we conjecture that they do not share this "Achilles heel" problem with Bacterial initiator tRNAs, but instead are efficiently processed at the 5′-end without any requirement for a 3′-end CCA sequence. This is consistent with our observation that initiator tRNA genes in Archaea do not have a particularly high frequency of CCA-templating.…”

“…This is because initiator tRNAs contain features that distinguish them from elongator tRNAs in highly conserved and domain-specific ways [21]. As shown in Tables 2, 3 and 4, our initiator tRNA gene predictions confirm and extend previously described rules and exceptions for bacterial initiator tRNA genes [21], including distinct patterns of mismatching at coordinates 1 and 72 in the acceptor stem (Table 2), distinct nucleotide frequencies at the 11:24 base-pair in the D-stem (Table 3), and unique anticodon-stem statistics at positions 29-31 and 39-41 (Table 4). Furthermore, our results are robust to missing data.…”

Evolution of initiator tRNAs and selection of methionine as the initiating amino acid

“…[2][3][4][5] Though the 'RNA-world' hypothesis is well accepted, the successive events in tRNA evolution are highly controversial but a coveted field of research. [6][7][8][9][10][11][12] Of the 2 (monophyletic and polyphyletic) theories of tRNA evolution, the monophyletic theory proposes that the tRNA (and therefore the different segments in it) originated as a single unit, whereas the polyphyletic theory argues that 2 segments of the modern tRNA, the anticodon-dihydrouridine (DHU) arm (A-D), and the acceptor-TcC arm (minihelix) regions (Fig. S1), originated separately, and then over the course of evolution converged into a single entity.…”