MBE Advance Access published online on October 9, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn225
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Research Article |
Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region
1 Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal
2 Faculdade de Ciências da Universidade do Porto, Portugal
3 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
4 Medical Faculty, University of Porto, Portugal
5 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Corresponding author: Filipe Pereira, IPATIMUP, R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal, Phone: +351 22 5570700, Fax: +351 22 5570799, Email: fpereira{at}ipatimup.pt
Received for publication October 1, 2008. Revision received October 1, 2008. Accepted for publication October 2, 2008.
A combined effect of functional constraints and random mutational events is responsible for the sequence evolution of the human mitochondrial DNA (mtDNA) control region. Most studies targeting this noncoding segment usually focus on its primary sequence information disregarding other informative levels such as secondary or tertiary DNA conformations. In this work, we combined the most recent developments in DNA folding calculations with a phylogenetic comparative approach in order to investigate the formation of intra-strand secondary structures in the human mtDNA control region. Our most striking results are those regarding a new cloverleaf-like secondary structure predicted for a 93 bp stretch of the control-region 5’ peripheral domain. Randomized sequences indicated that this structure has a more negative folding energy than the average of random sequences with the same nucleotide composition. In addition, a sliding window scan across the complete mitochondrial genome revealed that it stands out as having one of the highest folding potential. Moreover, we detected several lines of evidence of both negative and positive selection on this structure with high levels of conservation at the structure-relevant stem regions and the occurrence of compensatory base changes in the primate lineage. In the light of previous data we discuss the possible involvement of this structure in mtDNA replication and/or transcription. We conclude that maintenance of this structure is responsible for the observed heterogeneity in the rate of substitution among sites in part of the human hypervariable region I, and that it is a hotspot for the 3’end of human mtDNA deletions.
Key Words: mtDNA control region • secondary structures • mutational heterogeneity • mtDNA deletions