Thirteen-exon-motif signature for vertebrate nuclear and mitochondrial type IB topoisomerases

Abstract

DNA topoisomerases contribute to various cellular activities that involve DNA. We previously identified a human nuclear gene that encodes a mitochondrial DNA topoisomerase. Here we show that genes for mitochondrial DNA topoisomerases (type IB) exist only in vertebrates. A 13-exon topoisomerase motif was identified as a characteristic of genes for both nuclear and mitochondrial type IB topoisomerases. The presence of this signature motif is thus an indicator of the coexistence of nuclear and mitochondrial type IB DNA topoisomerases. We hypothesize that the prototype topoisomerase IB with the 13-exon structure formed first, and then duplicated. One topoisomerase specialized for nuclear DNA and the other for mitochondrial DNA.

Figure 1

Alignment of the amino acid sequences of top1mt proteins. (A) Alignment of the sequences encoded by the first exon of the genes for the five identified mitochondrial topoisomerases I. (B) Alignment of the sequences encoded by the last 13 exons of the genes for the five mitochondrial (mt) and corresponding nuclear (n) topoisomerases I. Residues encoded by each exon are marked by solid or open bars above the sequences; exon numbers for the mitochondrial and nuclear enzymes are outside and inside the parentheses, respectively. The catalytic tyrosine (Y) is marked with an asterisk and the critical basic amino acids (RKR) are marked with plus signs.

Figure 2

Fluorescence in situ hybridization analysis demonstrating the location of the Mm-TOP1mt gene at bands E2–E3 on chromosomes 15. Both chromosomes with symmetrical FITC signals on sister chromatids are identified by arrows.

Figure 3

Cluster analysis of the mitochondrial and nuclear topoisomerases I. The amino acid sequences encoded by the 13-exon topoisomerase motif of vertebrate genes for nuclear (blue bracket) and mitochondrial (red bracket) enzymes (Fig. 1B) were used for this analysis. For the other enzymes (green bracket), the corresponding regions, based on sequence alignment and size, were used. Hs, H.sapiens; Rn, R.norvegicus; Mm, M.musculus; Gg, G.gallus; Dr, D.rerio; Ci, C.intestinalis; Dm, D.melanogaster; Ce, C.elegans; Sp, S.pombe; Sc, S.cerevisiae; At, A.thaliana; Os, O.sativa. The bar indicates the scale for 10% dissimilarity between amino acid sequences.