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Cryptic tRNAs in chaetognath mitochondrial genomes

Paper ID Volume ID Publish Year Pages File Format Full-Text
14920 1361 2016 14 PDF Available
Title
Cryptic tRNAs in chaetognath mitochondrial genomes
Abstract

•Chaetognath mitogenomes exhibit more than one tRNA-like sequence as previously suggested.•16S rRNA genes appear as chaetognath tRNA nurseries.•TRNA pairs seem templated by sense-antisense strands as previously suggested for multifunctional ribosomal-like protogenomes.

The chaetognaths constitute a small and enigmatic phylum of little marine invertebrates. Both nuclear and mitochondrial genomes have numerous originalities, some phylum-specific. Until recently, their mitogenomes seemed containing only one tRNA gene (trnMet), but a recent study found in two chaetognath mitogenomes two and four tRNA genes. Moreover, apparently two conspecific mitogenomes have different tRNA gene numbers (one and two). Reanalyses by tRNAscan-SE and ARWEN softwares of the five available complete chaetognath mitogenomes suggest numerous additional tRNA genes from different types. Their total number never reaches the 22 found in most other invertebrates using that genetic code. Predicted error compensation between codon-anticodon mismatch and tRNA misacylation suggests translational activity by tRNAs predicted solely according to secondary structure for tRNAs predicted by tRNAscan-SE, not ARWEN. Numbers of predicted stop-suppressor (antitermination) tRNAs coevolve with predicted overlapping, frameshifted protein coding genes including stop codons. Sequence alignments in secondary structure prediction with non-chaetognath tRNAs suggest that the most likely functional tRNAs are in intergenic regions, as regular mt-tRNAs. Due to usually short intergenic regions, generally tRNA sequences partially overlap with flanking genes. Some tRNA pairs seem templated by sense-antisense strands. Moreover, 16S rRNA genes, but not 12S rRNAs, appear as tRNA nurseries, as previously suggested for multifunctional ribosomal-like protogenomes.

Keywords
tRNA; Chaetognatha; Cryptic tRNA; Overlap coding; tRNA misloading
First Page Preview
Cryptic tRNAs in chaetognath mitochondrial genomes
Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 62, June 2016, Pages 119–132
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering