Phylogenetic relationship

The potential complications of inferring phylogeny from molecular data have also been emphasized by studies of Ebola virus. One protein, the fusion glycoprotein gp2, showed structural homology to viruses that were quite unrelated (Malashkevich et al, 1999 Weissenhorn et al, 1998), whereas another, the matrix protein, showed no homology even to its closest relatives (Dessen et al, 2000). 

With increasing sequence data, there are now several bases on which to construct phylogenies. However, there is not yet a satisfactory phylogenetic classification that encompasses all viral families. Three-dimensional structure will continue to play a pivotal role as new viral families are explored. Such comparative studies are not just of academic importance. Beginning to understand the mechanisms of viral evolution is an important part of understanding how new viruses and their associated diseases emerge (Condit, 2001). 

was supported by the American Cancer Society (RPG-99-365-01-GMC) and National Institutes of Health (R01-GM66875), and L.L. was supported by the Swedish Natural Science Research Council. M.S.C. wishes to thank Michael Rossmann, his postdoctoral mentor, for introducing him to virus structme, and several colleagues in the years since whose discussions have maintained this interest Jack Johnson, Lee Makowski, and Don Caspar. 

Agbandje-McKenna, M., Llamas-Saiz, A. L., Wang, F., Tattersall, P., and Rossmann, M. G. (1998). Structured, 1369-1381. 

Branden, C.-l., and Tooze, J. (1998). Introduction to Protein Structure. Garland, New York. 

The difficulties in assigning function to a P450 solely based on its amino acid sequence will be partly alleviated as more catalytic functions become known and diagnostic sequence elements identified. The matter is particularly complicated for the A-type P450s involved in natural product synthesis. Plants are known to produce more than 

The wide diversity in amino acid sequences found among the P450s is evident by the fact that in A. thaliana, P450s belong to 45 of the 59 plant P450 families. 

---

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... 

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. 3. Phylogenetic relationship of strain BMEL-2 and related taxa, based on D1/D2 region sequence of the large-subunit rDNA. Bar, 0.01 nucleotide substitution per position.

Bakker, E. T., Yassibades, D. D., Morton, C. and Savolainen, V. 1998. Phylogenetic relationships of Biebersteinia Stephan (Geraniaceae) inferred from rbcL and utpB sequence comparisons. Bot. J. Linn. Soc. 127 149-158. 

Nyffeler, R. 2002. Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from tmK/matK and trnL-trnF sequences. Amer. J. Bot. 89 312-326. 

Hibsch-Jetter, C. 2001. Phylogenetic relationships in Chrysosplenium (Saxifragaceae) based on analysis of a combined rbcUmatK sequence data set. Amer. J. Bot. 88 883-893. 

Rosche B, B Tshisuaka, B Hauer, F Lingens, S Fetzner (1997) 2-Oxo-l,2-dihydroquinoline 8-monooxygen-ase phylogenetic relationship to other multicomponent nonheme iron oxygenases. J Bacterial 179 3549-3554. 

The siderochromes recorded in Table 2 constitute a selected group and represent only about half of the total number of these substances isolated to date. However, these representatives display sufficient diversity in structure and in distribution to provide clues about their phylogenetic relationships. 

Chilton, N.B., Gasser, R.B. and Beveridge, I. (1997a) Phylogenetic relationships of Australian strongyloid nematodes inferred from ribosomal DNA sequence data. InternationalJournal for Parasitology 27,1481-1494. 

Okamoto, M., Bessho, Y., Kamiya, M., Kurosawa, T. and Horii, T. (1995) Phylogenetic relationships within Taenia taeniaeformis varian Is and other taeniid cestodes inferred from the nucleotide sequence of the cytochrome c oxidase subunit I gene. Parasitology Research 81, 451-458. 

Fig. 16.3. Phylogenetic relationships between the predicted amino acid sequence of As-p18 and cLBPs from other sources. Asterisked ( ) proteins possess secretory leader/signal sequences. The percent identity of each protein with As-p18 is shown in parenthesis. Protein sequences from C. elegans and C. briggsae are prefixed Ce and Cb , respectively. It is clear that cLBP-like proteins from nematodes fall into two groups - one group whose members have secretory leaders, and those with no such leader - and cLBPs from vertebrates fall into the latter group. Reproduced from Plenefisch etal., 2000, with permission.

Rosche, B. Tshisuaka, B. Hauer, B., et al., 2-Oxo-l,2-Dihydroquinoline 8-Monooxygenase, Phylogenetic Relationship to other Multicomponent Nonheme Iron Oxygenases. J. Bacteriol, 1997. 179(11) pp. 3549-54. 

Oatps/OATPs were newly classified within the OATP (protein)/SLCO (gene) (human) and Oatp (protein)AS7co (gene) (rodents) superfamily according to their phylogenetic relationships and chronology of identification. The methods of classification and the nomenclature were described in detail in a recent review [21],... 

Cladistics Method of classification employing genealogies alone in inferring phylogenetic relationships among organisms (see also Phylogeny). 

Peterson SW et ai, Penicillium coffeae, a new endophytic species isolated from a coffee plant and its phylogenetic relationship to P. fellutanum, P. thiersii and P. brocae based on parsimony analysis of multilocus DNA sequences, Mycologia 97 659-666, 2005. 

There are numerous computer software programs that permit one to investigate sequence ahgnment and phylogenetic relationships among (a) various proteins, domains, motifs, modules, etc., and (b) nucleic acid sequences in DNA and RNA. In addition to those presented below, various Internet-based algorithms afford rapid and convenient analysis of macromolecular sequences. 

---