BMC Genomics 2005, 6:136 http://www.biomedcentral.com/1471-2164/6/136 Table 1: The number of genes that obey the rules of mitochondrial pyrimidine-purine base composition. All oxidative phosphorylation complex protein genes were included as membrane protein genes. Soluble mitochondrial protein genes included those of ribosomal proteins, maturases and endonucleases from intronic ORFs, and polymerase-like proteins. Unknown ORFs, hypothetical proteins, and proteins of unknown localization were excluded from the analysis. Transcripts that do not follow Rule #1 include almost all Dictyostelium transcripts, Chondrus crispus SDH2, Porphyra purpurea SDH2, COX2, and ymf39, Marchantia polymorpha NAD7 and ATPa, and Arabidopsis NAD7, NAD9, and ATP1. The Chlamydomonas reinhardtii rtl transcript breaks Rule #3. Organism Name Rule 1 Rule 2 Rule 3 Genbank Accession Latin Common Holds (Fails) Holds (Fails) Holds (Fails) [NC_001807] [NC_005089] [NC_001913] [NC_002008] [NC_000845] [NC_001323] [NC_002784] [NC_001573] [NC_002333] [NC_001709] [NC_002074] [NC_003344] [NC_001453] [NC_000933] [NC_001328] [NC_001224] [NC_001326] [NC_000895] [NC_001677] [NC_002007] [NC_001638] [NC_000892] [NC_001660] [NC_001284] Homo sapiens Mus musculus Oryctolagus cuniculus Canis familiaris Sus scrofa Gallus gallus Dromaius novaehollandiae Xenopus laevis Danio rerio Drosophila melanogaster Rhipicephalus sanguineus Thyropygus sp. DVL-2001 Strongylocentrot. purpuratus Metridium senile Caenorhabditis elegans Saccharomyces cerevisiae Schizosaccharomyces pombe Dictyostelium discoideum Chondrus crispus Porphyra purpurea Chlamydomonas reinhardtii Pedinomonas minor Marchantia polymorpha Arabidopsis thaliana Human Mouse Rabbit Dog Pig Chicken Emu Frog Zebrafish Fruit fly Brown dog tick Giant millipede Sea urchin Brown sea anemone Soil nematode Baker's yeast Fission yeast Slime mold Irish moss/Red algae Seaweed/Red algae Green algae Green algae Liverwort Thale cress 12 (1) 12 (1) 12 (1) 13 13 13 13 13 13 13 13 13 13 13 12 7 6 2(13) 18(1) 16(3) 7 11 13(2) 19(3) 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 (1) 3 2 2 2 (1) 2 11(3) 3 3 2 (1) - - - - - - - - - - - - - 1 - 11 - 14 5 6 0(1) - 17 8 Hypothetical Proteins or Unknown Localization - - - - - - - - - - - - - - - 1 4 11 1 6 - - 43 87 few exceptions to these rules. In some mammals (though not all) the ND6 transcript does not follow rule #1. The main exception for rule #2 is the large ribosomal RNA subunit in C. elegans, which has almost equal numbers of purines and pyrimidines. In other non-animal species the short 5S rRNA sometimes contains more pyrimidines than purines. We examined the mtDNA from 8 species that encode genes for both soluble and membrane proteins. In Figure 3A we plot the percent pyrimidine in the transcripts versus the frequency at which transcripts of that type (soluble proteins, membrane proteins, or rRNA) occur in the 8 spe- cies. The membrane protein transcripts had a distinctive distribution with a peak at around 56 % pyrimidine. The ribosomal RNA and soluble protein transcripts had over- lapping distributions with peaks near 45 % and 47 % pyri- midine respectively. These data explain the signals obtained in the pyrimidine-purine walks. It also gives an explanation as to why the soluble protein transcript walks are more variable than the membrane protein transcript walks, since the purine-rich signal is weaker in soluble protein transcripts than is the pyrimidine-rich signal in the membrane protein transcripts. The relative pyrimidine percentage at each codon position in membrane and sol- uble protein transcripts is shown in Figures 3B and 3C will be discussed later. To clearly illustrate the relationship between protein hydrophobicity and the pyrimidine content of the genes, we plot in Figure 4 the percent pyrimidine in the protein transcript versus the grand average of hydropathicity (GRAVY) of the protein for four species with numerous mitochondrial-encoded soluble and membrane protein genes. A higher GRAVY score indicates a higher hydropho- bicity of the protein. There was a strong correlation (P < 0.001) between the percent pyrimidine and the hydro- phobicity of the encoded protein. This correlation has Page 5 of 12 (page number not for citation purposes)