Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of <it>Dolichopoda </it>cave crickets (Orthoptera, Rhaphidophoridae)

• Main Authors: Venanzetti Federica, Johnsen Arild, Martinsen Lene, Bachmann Lutz
• Format: Article
• Language: English
• Published: BMC 2010-01-01
• Series: BMC Evolutionary Biology
• Online Access: http://www.biomedcentral.com/1471-2148/10/3

<p>Abstract</p> <p>Background</p> <p>The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the <it>pDo500 </it>sequence family in <it>Dolichopoda </it>cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat.</p> <p>Results</p> <p>We assessed the phylogenetic footprints of the HH ribozyme within the <it>pDo500 </it>sequences from 38 different populations representing 12 species of <it>Dolichopoda</it>. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the <it>pDo500 </it>repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the <it>Dolichopoda </it>populations and species.</p> <p>Conclusions</p> <p>The phylogenetic footprints suggest that the HH region of the <it>pDo500 </it>sequence family is selected for function in <it>Dolichopoda </it>cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to <it>trans </it>cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in <it>Dolichopoda </it>is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.</p>