BMC Genomics 2005, 6:136 http://www.biomedcentral.com/1471-2164/6/136 PFyigriumriedi5ne-purine codon position walks of select mitochondrial-encoded transcripts Pyrimidine-purine codon position walks of select mitochondrial-encoded transcripts. (A) Membrane protein tran- script, human COX1 (C) Soluble protein transcript, Chondrus crispus ribosomal protein S12. For each codon position step, the x-axis was incremented by 3 for comparison to the complete transcript. A pyrimidine-purine walk of (B) human 16S ribosomal RNA is also shown for comparison. of the gene. The mitochondrial-encoded transcripts from other species have a similar pattern of pyrimidine-rich- ness in the three codon positions (see Figures 3B and 3C and Table 2). In mtDNA-encoded membrane-protein transcripts, codon position 2 contains the most pyrimi- dines, as predicted (Figure 3B). However, codon position 3 also contributes slightly to the pyrimidine-rich signal while codon position 1 is often slightly purine-rich. In the soluble ribosomal protein transcript the purine-rich sig- nal is driven mainly by codon position 1, while codon positions 2 and 3 contribute only slightly (see also Figure 3B). The eight known mtDNA-encoded soluble protein transcripts from Arabidopsis give a similar purine-rich sig- nal in pyrimidine-purine walks (see additional file 1: Fig- ure S1). Even the signals of the individual codon positions follow the same trends in all eight genes. As an example of the robustness of this signal, pyrimidine- purine walks of each codon position from the other 12 human mtDNA protein-coding genes are shown in Figure 6. From the linearity of the walk of the entire genome in Figure 1, it is clear that the signal strength is almost constant through all protein-coding genes. The pyrimidine-rich signal is driven by codon position 2 in almost all cases, with position 3 contributing modestly and codon position 1 not contributing to an appreciable extent. The conservation of this pattern through the vast majority of the mitochondrial transcripts indicates the strong selective pressure for this signature. Unlike the other transcripts, the ND6 transcript is purine-rich, but it is also the only transcript encoded on the (+) light strand of mtDNA. So there does appear to be a strand-specific selective force present as well, in human mtDNA. How- Page 8 of 12 (page number not for citation purposes)