Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

Abstract

Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading ‘pseudogenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.

Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats

“…The boundaries of the ribosomal genes rrnL and rrnS were assumed to extend to the boundaries of flanking genes as the ends of ribosomal genes were difficult to be precisely determined by DNA sequencing alone (Boore, 2006). Identification and positional confirmation of the tRNAs was accomplished by using the software of MITFI (Juhling et al., 2012) and ARWEN (Laslett & Canback, 2008). …”

Genetic aspects of mitochondrial genome evolution

“…In Onychophora elaborate editing is capable of repairing large tRNA fragments (Segovia et al, 2011). Aberrant tRNAs structures have been collected and studied systematically as part of a recent effort to re-annotate mitochondrial tRNAs (Jühling et al, 2012a). Like their nuclear counterparts, mt-tRNAs are chemically modified.…”

“…Marsupials are well known to have lost mt-tRNA-Lys (Dörner et al, 2001). For a recent comprehensive overview of tRNA losses we refer to (Jühling et al, 2012a), see also (Gissi et al, 2008). The protein coding gene that is missing most often is atp8.…”

“…Remnants of such pro-16 cesses have been detected for instance as non-coding regions at positions where the deleted genes would be expected (Arndt and Smith, 1998) or as pseudogenes (Macey et al, 1997). Recently a large scale study on tRNAs provided numerous examples of pseudogenisation supporting duplication and inverse duplication based mechanisms (Jühling et al, 2012a). The presence of multiple functional copies after a duplication can facilitate tRNA recruitment, i.e.…”

Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustaceanArmadillidium vulgare

“…Metazoan mt tRNAs often appear degenerated, without the complete cloverleaf secondary structure: absence of the highly conserved D-loop and/or T-loop and even complete arms renders their detection problematic. 14,15 As a matter of fact, in addition to the classical tool tRNAscan-SE 16 that detects cloverleaf structures, other more specialized tools such as ARWEN 17 and MiTFi 14 were developed to significantly improve metazoan mt tRNA gene identification. Moreover, tRNA genes can also be missed because of extensive RNA editing that modifies the RNA sequence as compared to the genomic DNA sequence.…”