Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison.

Abstract

Comparison of the amino acid sequences of eight proteins from the soil amoeba Dicyostelium discoideum to those of their homologs in bacteria, yeast, and other eukaryotes indicates that Dictyostelium diverged from the line leading to mammals at about the same time as the plant/animal divergence. Yeast appear to have diverged considerably earlier. It is argued that previous analyses indicating that D. discoideum diverged before yeast were misleading because of the nature of the small ribosomal subunit rRNA sequences used in these studies. We suggest that amino acid sequences may be more reliable than untranslated nucleic acid sequences for evolutionary comparisons, especially among organisms with significant skewing of their A+T content.Comparison of the primary sequences in RNA of the small ribosomal subunit in a variety of organisms has given some indication of the phylogenetic relationships of metazoa, protists, and bacteria (1-3). The monophyletic origin of all eukaryotes is unequivocally demonstrated by the close relationships of their 18S rRNA sequences relative to those of both eubacteria and archaebacteria. An early branch along the eukaryote limb was found in the protist Dictyostelium discoideum. Based on the 18S rRNA sequence, D. discoideum is more diverged from vertebrates than the yeast Saccharomyces cerevisiae (1). However, when the amino acid sequence of the pyrimidine biosynthetic enzyme dihydroorotase [(S)-dihydroorotate amidohydrolase, EC 3.5.2.3] was compared to that in hamsters and S. cerevisiae, the D. discoideum sequence was found to be more closely related to that of the mammalian enzyme than that of the yeast (4). This contradiction results from comparison of untranslated nucleic acid sequences on the one hand and comparison of amino acid sequences on the other. While the primary sequence of D. discoideum 18S rRNA differs 27% from that of the amphibian Xenopus laevis, the predicted secondary structures of these rRNAs are almost identical (5). This suggests that compensatory base changes have occurred in different portions ofthe molecule such that the stem-loop structures are preserved. Like much of the genomic DNA in Dictyostelium that does not encode proteins, the 18S rRNA-encoding DNA of Dictyostelium has an unusually high A+T content: total genomic DNA, A+T = 85%; 18S rRNAencoding DNA, A+T = 57% (1, 6). This can be compared to 18S rRNA-encoding DNA in X. laevis where A+T = 46%. It appears that there has been selection for high A+T content where it is compatible with function in Dictyostelium. Since the function of 18S rRNA is chiefly dependent on secondary structure, compensatory mutations can be accepted. When comparing the nucleic acid sequences of 18S rRNA of Dictyostelium aligned to those of Xenopus, it can be seen that there have been almost 3 times as many conversions of guanine or cytosine to adenine or thymine as the converse (G or C -* A or T = 291; A or T --G or C = 98). Yet a majority of the conversions are compensatory, such that intramolecular bonds that form the seco...

Dictyostelium Finds New Roles to Model

“…This reassessment confirmed earlier work, suggesting that the ancestor of Dictyostelium diverged from the ancestors of animals and fungi at some time after the divergence of ancestral plants (Loomis and Smith 1990;Baldauf and Doolittle 1997). Thus Dictyostelium is more closely related to present-day animals than are plants (Figure 1).…”

Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria

“…One reason for using the protein sequences is that composition or codon-usage bias in DNA is a confounding factor in construction of phylogenetic trees (Loomis and Smith 1990;Hasegawa and Hashimoto 1993;Lockhart et al 1992;He and Haymer 1995). Another reason is that natural selection tends to lessen the effects of nucleotide bias.…”

“…In a phylogenetic context, protein sequences are often considered more useful than DNA sequences because they can be immune to base compositional differences occurring in the latter, and so phylogenetic information would be unaffected in the protein sequence (Loomis and Smith 1990; Hasegawa and Hashimoto 1993; Hashimoto et al 1995). However, the evidence presented above does suggest that protein sequences are not always immune to compositional differences in the DNA, and this could have an effect on the success of phylogenetic analysis (Steel et al 1993(Steel et al , 1995.…”

Base Compositional Bias and Phylogenetic Analyses: A Test of the “Flying DNA” Hypothesis

“…Extreme base compositional biases have been shown to confound phylogenetic relationships for some molecular phylogenetic studies (Penny et al, 1990;Sidow and Wilson, 1990;Loomis and Smith, 1992;Forterre et al, 1993;Hasegawa and Hashimoto, 1993;Lockhart et al, 1992aLockhart et al, ,b, 1994. Log-determinant (ϭparalinear) distances were developed to account for changes in base composition among taxa in a phylogenetic analysis (Steel, 1994;Lockhart et al, 1994;Lake, 1994).…”

“…Examples of base compositional bias confounding phylogenetic relationships have been reported for studies on the origin of photosynthetic organelles (Lockhart et al, 1992a,b) and trees of life (Loomis and Smith, 1992;Sogin et al, 1993). Here we examine the extent of potential effects of base compositional bias in the estimation of relationships among bats, primates, and other mammals.…”