MAMMALIAN MITOCHONDRIAL D-LOOP REGION STRUCTURAL-ANALYSIS - IDENTIFICATION OF NEW CONSERVED SEQUENCES AND THEIR FUNCTIONAL AND EVOLUTIONARYIMPLICATIONS

This paper reports the first comprehensive analysis of Displacement lo op (D-loop) region sequences from ten different mammalian orders. It r epresents a systematic evolutionary study at the molecular level on re gulatory homologous regions in organisms belonging to a well defined c lass, mammalia, which radiated about 150 million years ago (Mya). We h ave aligned and analyzed 26 complete D-loop region sequences available in the literature and the fat dormouse sequence, recently determined in our laboratory. The novelty of our alignment consists of the extens ive manual revision of the preliminary output obtained by computer pro gram to optimize sequence similarity, particularly for the two periphe ral domains displaying heterogeneity in length and the presence of rep eated sequences. The multialignment is available at the WWW site: http ://www.ba.cnr.it/dloop.html. Our comparative study has allowed us to i dentify new conserved sequence blocks present in all the species under consideration and events of insertion/deletion which have important i mplications in both functional and evolutionary aspects. In particular we have detected two blocks, about 60 bp long, extended termination a ssociated sequences (ETAS1 and ETAS2) conserved in all the organisms c onsidered. Evaluation against experimental work suggests a possible fu nctional role of ETAS1 and ETAS2 in the regulation of replication and transcription and targeted experimental approaches. The analyses on co nserved sequence blocks (CSBs) clearly indicate that CSB1 is the only very essential element, common to all mammalian mt genomes, while CSB2 and CSB3 could be involved in different though related functions, pro bably species specific, and thus more linked to nuclear-mitochondrial coevolutionary processes. Our hypothesis on the different functional i mplications of the conserved elements, CSBs and TASs, reported so far as main regulatory signals, would explain the different conservation o f these elements in evolution. Moreover the intra-order comparison of the D-loop regions highlights peculiar features useful to define the e volutionary dynamics of this region in closely related species. (C) 19 97 Elsevier Science B.V.