1. Initiator tRNA Genes Template the 3′ CCA End at High Frequencies in Bacteria
- Author
-
Ardell, David H. and Hou, Ya-Ming
- Subjects
0301 basic medicine ,Medical and Health Sciences ,Genome ,Genes, Archaeal ,chemistry.chemical_compound ,Databases, Genetic ,RNA Precursors ,Protein biosynthesis ,Base Pairing ,Genetics ,0303 health sciences ,Selenocysteine ,030302 biochemistry & molecular biology ,Bacterial ,Biological Sciences ,Transfer RNA ,Met ,cardiovascular system ,Research Article ,Biotechnology ,Genome evolution ,RNA, Transfer, Met ,Bioinformatics ,information science ,Pyrrolysine ,Biology ,Initiator tRNA ,Databases ,03 medical and health sciences ,Genetic ,Information and Computing Sciences ,parasitic diseases ,Anticodon ,cardiovascular diseases ,CCA ,Gene ,030304 developmental biology ,030102 biochemistry & molecular biology ,Bacteria ,Base Sequence ,fungi ,biology.organism_classification ,Archaea ,Transfer ,030104 developmental biology ,Genes ,chemistry ,Genes, Bacterial ,Archaeal ,RNA - Abstract
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 precursor pools. 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3314-x) contains supplementary material, which is available to authorized users.
- Published
- 2015