10.21425/NXQC-VK37
Ardell, David H.
Hou, Ya-Ming
Reannotation of CCA-ends, initiator tRNAs, and other CAU-anticodon tRNAs
of prokaryotic genomes in tRNAdb-CE 0.8
UC Merced
2016
initiator tRNA
prokaryotic genomes
CCA ends
tRNAdb-CE
CAU anticodon
2016-10-27T12:19:43+00:00
Dataset
GICS-D-16-01058R1
44640152
Creative Commons Attribution 4.0 International (CC BY 4.0)
Background: While the CCA sequence at the mature 3′ end of tRNAs is
conserved and critical for translational function, a genetic template for
this sequence is not always contained in tRNA genes. In eukaryotes and
archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by
CCA-adding enzymes. In bacteria, tRNA genes template CCA sporadically.
Results: In order to understand the variation in how prokaryotic tRNA
genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database
version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes
template CCA at the highest average frequency (74.1%) over all functional
classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100%
respectively). Across bacterial phyla and a wide range of genome sizes,
many lineages exist in which predominantly initiator tRNA genes template
CCA. Convergent and parallel retention of CCA templating in initiator tRNA
genes evolved in independent histories of reductive genome evolution in
Bacteria. Also, in a majority of cyanobacterial and actinobacterial
genera, predominantly initiator tRNA genes template CCA. We also found
that a surprising fraction of archaeal tRNA genes template CCA.
Conclusions: We suggest that cotranscriptional synthesis of initiator tRNA
CCA 3′ ends can complement inefficient processing of initiator tRNA
precursors, “bootstrap” rapid initiation of protein synthesis from a
non-growing state, or contribute to an increase in cellular growth rates
by reducing overheads of mass and energy to maintain nonfunctional tRNA
precursors. More generally, CCA templating in structurally non-conforming
tRNA genes can afford cells robustness and greater plasticity to respond
rapidly to environmental changes and stimuli.
CCA-end reannotation was done by automated sequence comparison to
annotated 5-prime end. Function of CAU-anticodon tRNAs was computed with
TFAM (Ardell and Andersson 2006) using the Silva model (Silva et al.
2007). Reannotations may be applied to prokaryotic genome data through
genome accession IDs provided in the sequence data identifiers.
Data were created with funding from the National Science Foundation,
Division of Behavioral and Cognitive Sciences under grant 1344279.