Phylogenetics

At this time, the photolyase/cryptochrome family has three members photolyase (cyclobutane pyrimidine dimer photolyase), (6-4) photolyase, and cryptochrome. A number of phylogenetic trees based on sequence comparisons of more than 100 members of the family across the three 

All plants tested so far, including AraUdopsis thaliana, tobacco, and soybean, do have photolyase. 

The (6—4) photolyase was first discovered in D. melanogaster (Todo et aL, 1993, 1996). Subsequently it was found in Xenopus laevis, rattlesnake (Kim et al, 1994), zebrafish, and A. thaliana, among many other species (Todo, 1999). Of special interest, the enzyme has not been found in birds and mammals (Hsu et at, 1996). Thus, humans lack both photolyase and (6-4) photo lyase and cannot carry out photorepair of UV-induced DNA damage. They rely solely on nucleotide excision repair for eliminating these potentially mutagenic and carcinogenic lesions from their DNA. 

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Hackstein et al ° have suggested that there may be a phylogenetic basis for the occurrence of significant methane formation in the gut of animals. It was argued that this refiected the presence of a methanogen receptor in the gut of animals which support large populations of these bacteria, since the production of... 

Woese, C. R., 1996. Phylogenetic trees Wliidier microbiology Current Biology 6 1060—1063. 

Furthermore, as shown in Figure 5.28, the number of amino acid differences between two cytochrome c sequences is proportional to the phylogenetic difference between the species from which they are derived. The cytochrome c in humans and in chimpanzees is identical human and another mammalian (sheep) cytochrome c differ at 10 residues. The human cytochrome c sequence has 14 variant residues from a reptile sequence (rattlesnake), 18 from a fish (carp), 29 from a mollusc (snail), 31 from an insect (moth), and more than 40 from yeast or higher plants (cauliflower). 

If a phylogenetic comparison is made of the 16S-Iike rRNAs from an archae-bacterium Halobacterium volcanii), a eubacterium E. coli), and a eukaryote (the yeast Saccharomyces cerevisiae), a striking similarity in secondary structure emerges (Figure 12.40). Remarkably, these secondary structures are similar despite the fact that the nucleotide sequences of these rRNAs themselves exhibit a low degree of similarity. Apparently, evolution is acting at the level of rRNA secondary structure, not rRNA nucleotide sequence. Similar conserved folding patterns are seen for the 23S-Iike and 5S-Iike rRNAs that reside in the... 

FIGURE 12.40 Phylogenetic comparison of secondary structures of 16S-Uke rRNAs from (a) a eubacterium (E. coli), (b) an archaebacterium (H. volcanii), (c) a eukaryote S. cerevisiae, a yeast). 

Studying evolutionary aspects, by the construction of phylogenetic trees from the pairwise differences between sequences for example, the classification with 70S, 30S RNAs established the separate kingdom of archaea... 

CNG channels are expressed in retinal photoreceptors and olfactory neurons, and play a key role in visual and olfactory signal transduction. In addition, CNG channels are found at low density in some other cell types and tissues such as brain, testis, and kidney. While the function of CNG channels in sensory neurons has been unequivocally demonstrated, the role of these channels in other cell types, where expression has been observed, remains to be established. Based on their phylogenetic relationship, the six CNG channels... 

Fredriksson R, Lagerstrom MC, Lundin LG et al (2003) The G-protein-coupled receptors in Hie human genome form five main families. Phylogenetic analysis, paralo-gon groups, and fingerprints. Mol Pharmacol 63 1256-1272... 

Histone Deacetylases (HDACs) catalyze the removal of the acetyl groups from lysines (see Fig. 1). Together with the HATs they are responsible for maintaining the level of histone acetylation throughout the genome. The family of HDAC proteins has been divided into four classes based on phylogenetic analysis and sequence comparison. HDACs of the classes I and II share the same Zn2+-based reaction and are evolutionary related. Class IV HDACs also possess a Zn2+-based reaction... 

Bjarnadottir TK, Gloriam DE, Hellstrand SH et al (2006) Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse. Genomics 88 263-273... 

Parallel arrays of microtubules are found in the axoneme of cilia and flagella of eukaryotic cells, and these are of constant pattern throughout the phylogenetic scale. 

Figure 1. An unrooted phylogenetic tree of the myosins based on the amino acid sequence comparison of their head domains demonstrating the division of the myosin superfamily into nine classes. The lengths of the branches are proportional to the percent of amino acid sequence divergence and a calibration bar for 5% sequence divergence is shovk n. The different classes of myosins have been numbered using Roman numerals in rough order of their discovery and hypothetical models of the different myosin structures are shown. Question marks indicate either hypothetical or unknown structural features, and only a fraction of the known myosins are shown. (Taken, in modified form, from Cheney et al., 1993).

Figure 2. Universal phylogenetic tree determined from rRNA sequence comparisons. A matrix of evolutionary distances (99) was calculated from an alignment (260) of representative 16S RRNA sequences from each of the three urkingdoms. The length of the lines is proportional to the phylogenetic difference. (Reproduced with permission from ret 16. Copyright 19. American Society for Microbiology.)...

Table 3-3 Major phylogenetic groups of living organisms... 

Fig. 8. Phylogenetic analysis of 16S rDNA sequence of the isolate V 33 (Tanamool et al, 2011)...

Figure 1 shows the phylogenetic relationship of the mitochondrial and bacterial Rieske proteins. Plant mitochondrial Rieske proteins form a separate cluster, whereas bacterial Rieske proteins are more closely related to Rieske proteins from fungi or mammals, although the subunit composition and organization of the bci complex is compa-... 

Fig. 1. (a) Schematic representation of the three types of anoxygenic ([1] and [2]) and oxygenic ([3]) photosynthesis found in plants and bacteria, (b) Phylogenetic tree based on 16S-rRNA sequence comparisons featuring only photo synthetic phyla. 

To date, only two exceptions to the pK of 8 rule have been found the Rieske protein from Sulfolobus acidocaldarius (139) and that from Thiobacillus ferrooxidans (140). In both cases, a first pK is observed in the vicinity of 6 (Fig. 7). The fact that Sulfolobus and Thiobacillus are phylogenetically almost as distant as they can possibly be, but share acidophilic growth conditions (medium-pH of 2), indicates that the pK, which is lower by 2 pH units in Sulfolobus and Thiobacillus, reflects adaptation. In the absence of structural information for the two acidophilic Rieske proteins, the molecular modifications resulting in this pK shift are difficult to guess. The absence of sequence data for the Thiobacillus protein furthermore precludes a comparative approach. It seems likely, however, that the solvent-exposed histidine ligands to the cluster will become slightly more bur-... 

FIGURE 1.2 An abbreviated version of the P450 phylogenetic tree compared with an evolutionary timescale (Lewis 1996). The dashed line represents a plot of evolutionary distance (Nelson and Strobel 1987). 

Walker, C.H., Bentley, P, and Oesch, F. (1978). Phylogenetic distribution of epoxide hydratase in different vertebrate species, strains, and tissues using three substrates. Biochemica et Biophysica Acta 539, 427 34. 

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