Phylogenetic tree cytochrome

Fig. 4-12 Phylogenetic tree constructed from amino acid sequences of cytochrome c.

Figure 4 Cytochrome P450 superfamily phylogenetic tree showing major gene families.

The resemblance among cytochrome c molecules extends to the level of amino acid sequence. Because of the molecule s relatively small size and ubiquity, the amino acid sequences of cytochrome c from more than 80 widely ranging eukaryotic species were determined by direct protein sequencing by Emil Smith, Emanuel Margoliash, and others. Comparison of these sequences revealed that 26 of 104 residues have been invariant for more than one and a half billion years of evolution. A phylogenetic tree, constructed from the amino acid sequences of cytochrome c, reveals the evolutionary relationships between many animal species (Figure 18.24). 

A feasible phylogenetic tree can be compiled from a comparison of the amino acid sequences of various cytochrome oxidases and NO reductase [279] (Fig. 42). 

Fig. 42. Possible phylogenetic tree of bo2,laailcaailcbbi-X.yx>e cytochrome oxidases and related enzymes. The distance between branching points is not related to the temporal course of development but simply shows its possible sequence...

Fig. 16.5, Phylogenetic trees derived on the basis of distance metrics derived from differences in various local structural parameters at topologically equivalent positions in a family of homologous cytochrome structures...

Fio. 11. Phylogenetic tree of the eukaryotes, as deduced from amino acid sequence differences between cytochromes c. Adapted from reference H9. 

Fig. 12. Phylogenetic tree of the higher plants, deduced from their cytochrome sequences. Adapted from references lii-lH.

The 2 CYPIA proteins have been isolated from the livers of a number of animal species, purified, and shown to share extensive structural similarity and to display similar substrate specificity. The human orthologue of CYP1A2 has been isolated from liver and shown to metabolize the same substrates, and to play the same role in carcinogen activation, as the rodent proteins [9]. The human CYPlAl has not been purified but it has been expressed in mammalian cells like the rodent orthologue, it catalyses the oxidation of polycyclic aromatic hydrocarbons and the N-oxidation of aromatic amines [10]. This apparent similarity in substrate specificity between the human and rodent CYPIA proteins would indicate that where CYPIA is involved, toxicological data can, in principle, be extrapolated to man with more confidence. Of the cytochrome P450 proteins so far characterized, the CYPl family appears to be the most conserved within the phylogenetic tree [11]. 

Figure 4.3 Phylogenetic tree of indole-3-gIycerole phosphate lyases and cytochrome P450 enzymes involved in henzoxazinoid biosynthesis.

Phylogenetic tree of purple photosynthetic bacteria have recently been suggested based on the sequence analyses of 16S ribosomal RNA (4.) We have determined the types of RC in many non-sulfur purple bacteria and considered about their occurrence in the phylogenetic tree. It seems that the ancestral purple bacteria had the RC with the cytochrome subunit and the subunit has been lost mutationally at least in four independent lines. 

Evolutionary Relationships of RC The types of RC complexes, in terms of the presence or absence of the cytochrome subunit, are summarized in Fig. 4-f together with the type of soluble cytochrome C2 and quinone species in the membrane. The phylogenetic tree was based on 16S ribosomal RNA sequence (4) and the information described above (7,8). 

The method was first applied (to the cytochromes c of a wide variety of species, from Neurospora to man) by Fitch and Maigoliash (69). The relatedness of two proteins of known sequence (mutation distance) is determined by the minimum number of nucleotide differences between the genes coding for the two polypeptides. A group of sequences (V, for example), can be compared, and the mutation distance between every pair determined. A phylogenetic tree is constructed from these values in such a manner as to minimize total mutation distances among all proteins in the sample. 

Fig. 7.7 Neighbor-joining phylogenetic tree of cytochrome bd subunit I homologues (CydA and CioA). Clades of cytochrome bd oxidase subunit I (CydA) could be separated from those of cyanide-insensitive oxidase subunit I (CioA). CydA clades are finlher separated into three large clades including Proteobacteria (a, p, y), Firmicutes, and Cyanobacteria, the CIO clade seems to be mixed up. Arrows [Escherichia coli, Azotobacter, Bacillus, Corynebacterium, Gluconobacter, and Pseudomonas) show the enzymes experimentally validated...

Phylogenetic tree of cytochrome c families (according to Dickerson and Timko-... 

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