This page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.

Protein Phylogeny

Alignments

To determine the relationship of the human GRM7 isoform a protein with its candidate homologs, listed on the Protein Homologs page, the sequences of these proteins were aligned on Phylogeny:fr using ClustalW, MUSCLE, and T-COFFEE (Edgar, 2000; Notredame, et al.,, 2000; Thompson, et al.,1994). The protein sequences were also aligned using AliBee - Multiple Alignment from the GeneBee website (Brodsky, et al., 1992; Brodsky, et al., 1993;Brodsky, et al., 1995; Nikolaev, et al., 1997). For all alignments, the default settings of the program were used (Brodsky, et al., 1992; Brodsky, et al., 1993;Brodsky, et al., 1995; Edgar, 2000; Nikolaev, et al., 1997; Notredame, et al.,, 2000; Thompson, et al.,1994).


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Phylogenetic Trees

To elucidate the evolutionary relationships between the human GRM7 protein and its candiate homologous proteins, the alignments generated by ClustalW, MUSCLE, T-COFFEE, and Ali-Bee Multiple Alignment were used to create phylogenetic trees (Brodsky, et al., 1992; Brodsky, et al., 1993;Brodsky, et al., 1995; Edgar, 2000; Nikolaev, et al., 1997; Notredame, et al.,, 2000; Thompson, et al.,1994). For each of the ClustalW, MUSCLE, and T-COFFEE alignments, two trees were created: one using Phlogeny:fr and one using TreeTop. The Phlyogeny:fr trees, which were created using either the ClustalW, MUSCLE, or T-COFFEE alignment and GBlocks, PhyML, and TreeDyn on the default settings, are shown in Figures 1, 3, and 5 (Anisimova, et al., 2006; Castresana, 2000; Chevenet, et al., 2008; Dereeper, et al., 2008; Edgar, 2000; Guindon, et al., 2003; Notredame, et al.,, 2000; Thompson, et al.,1994). The TreeTop trees, which were created using either the ClustalW, MUSCLE, T-COFFEE, or Ali-Bee Multiple Alignment and TreeTop on the default settings, are shown in Figure 2, 4, 6, and 7 (Brodsky, et al., 1992; Brodsky, et al., 1993;Brodsky, et al., 1995; Chumakov et al., 1988; Edgar, 2000; Nikolaev, et al., 1997; Notredame, et al.,, 2000; Thompson, et al.,1994; Yushmanov et al., 1988).

The phylogenetic trees created by the varying combinations of alignment and tree-generating programs do not all have the same topology; however, some general trends do emerge. One interesting trend is that the phylogenetic trees all show that human GRM7 protein is more closely related to the chimpanzee, mouse, rat, dog, and chicken GRM7 proteins than it is to the other human GRM proteins This suggests
that the GRM paralogs arose in a common ancestor to all of these species. Another interesting trend, albeit perhaps more expected, is that the human GRM family of proteins always cluster according to the group to which they belong: GRM1 and GRM5, which comprise Group I, are always found together; GRM2 and GRM3, which comprise Group II, are always found together; and finally, GRM4, GRM6, GRM7, and GRM8 are always found together (Entrez Protein, 2009). Additionally, as might be expected, all trees except the one built using AliBee show that the calcium-sensing receptor and taste receptor proteins are less related to the GRM7 protein than are the other proteins in the GRM family. Discrepencies between the topologies of the various trees are due the differences in the algorithms used for each of the alignment and tree building programs, as well as the differences in the settings used for each program.







Figure 1. Phylogenetic tree built using ClustalW, GBlocks, PhyML,  and TreeDyn. A tree was built from a ClustalW alignment of the human GRM7 isoform a protein and all its candidate homologous proteins using the Phylogeny:fr website(Anisimova, et al., 2006; Castresana, 2000; Chevenet, et al., 2008; Dereeper, et al., 2008; Guindon, et al., 2003; Thompson, et al., 1994).








Figure 3. Phylogenetic tree built using MUSCLE, GBlocks, PhyML,  and TreeDyn. A tree was built from a MUSCLE alignment of the human GRM7 isoform a protein and all its canidate homologous proteins using the Phylogeny:fr website(Anisimova, et al., 2006; Castresana, 2000; Chevenet, et al., 2008; Dereeper, et al., 2008; Edgar, 2000; Guindon, et al., 2003).








Figure 5. Phylogenetic tree built using T-COFFEE, GBlocks, PhyML,  and TreeDyn. A tree was built from a T-COFFEE alignment of the human GRM7 isoform a protein and all its candidate homologous proteins using the Phylogeny:fr website(Anisimova, et al., 2006; Castresana, 2000; Chevenet, et al., 2008; Dereeper, et al., 2008; Guindon, et al., 2003; Notredame, et al., 2000).



Figure 2. Phylogenetic tree built using ClustalW alignment and TreeTop. A tree was built from a ClustalW alignment of the human GRM7 isoform a protein and candidate homologous proteins using the TreeTop website (Brodsky, et al., 1992; Brodsky, et al., 1995; Chumakov et al., 1988; Thompson, et al.,1994; Yushmanov et al., 1988).




Figure 4. Phylogenetic tree built using MUSCLE alignment and TreeTop. A tree was built from a MUSCLE alignment of the human GRM7 isoform a protein and candidate homologous proteins using the TreeTop website (Brodsky, et al., 1992; Brodsky, et al., 1995; Chumakov et al., 1988; Edgar, 2000; Yushmanov et al., 1988).




Figure 6. Phylogenetic tree built using T-COFFEE alignment and TreeTop. A tree was built from a T-COFFEE alignment of the human GRM7 isoform a protein and candidate homologous proteins using the TreeTop website (Brodsky, et al., 1992; Brodsky, et al., 1995; Chumakov et al., 1988; Notredame, et al.,, 2000; 1994; Yushmanov et al., 1988).



Figure 7. Phylogenetic tree built by GeneBee's AliBee - Multiple Alignment. The protein sequences of the human GRM7 isoform a protein and its candidate homologs were input into AliBee - Multiple Alignment, which can be accessed from the GeneBee website. The tree generated from the alignment of these sequences is shown on the left (Brodsky, et al., 1992; Brodsky, et al., 1993;Brodsky, et al., 1995; Nikolaev, et al., 1997).








References

 References

 

Anisimova M., Gascuel O. (2006) Approximate likelihood ratio test for branchs: A fast, accurate and powerful alternative. Syst Biol. 55(4):539-52.

Brodsky L.I., Drachev A.L., Gorbalenya A.E., Leontovich A.M., Feranchuk S.I. (1993). A novel method of multiple alignment of bio-polymers (MA-Tools module of GeneBee package). Biosystems. 30:65-79.

Brodsky L.I., Ivanov V.V., Kalaidzidis Ya.L., Leontovich A.M., Nikolaev V.K., Feranchuk S.I., Drachev V.A. (1995). GeneBee-NET:Internet-based server for analyzing biopolymers structure. Biochemistry. 60(8): 923-928.

Brodsky L.I., Vasiliev A.V., Kalaidzidis Ya.L., Osipov Yu.S., Tatuzov R.L., Feranchuk S.I. (1992). GeneBee: the program package for biopolymer structure analysis. Dimacs. 8:127-139.

Castresana J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17(4):540-52.

Chevenet F., Brun C., Banuls AL., Jacq B., Chisten R. (2008) TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics. 7:439.

Chumakov K.M. and Yushmanov S.V. (1988) The maximum topological similarity principle in molecular systematics, Mol. Genet. Microbiol. Virusol. 3:3-9.

Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. (2008). Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36(Web Server issue):W465-9. *joint first authors

Edgar R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-7.

Entrez Protein. (2009). glutamate receptor, metabotropic 3 precursor [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=UKA0ZMG6016&log%24=prottop&blast_rank=7&list_uids=46358417.

Guindon S., Gascuel O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52(5):696-704.

Nikolaev V.K., Leontovich A.M., Drachev V.A., Brodsky L.I. (1997). Building multiple alignment using iterative analyzing biopolymers structure dynamic improvement of the initial motif alignment. Biochemistry. 62(6):578-582.

Notredame C., Higgins DG., Heringa J. (2000). T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302(1):205-17.

Thompson J.D., Higgins D.G., Gibson T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-80.

Yushmanov S.V. and Chumakov K.M. (1988). Algorithms of the maximum topological similarity phylogenetic trees construction, Mol. Genet. Microbiol. Virusol. 3:9-15 .

                                                                                                                   

Jennifer Wagner
wagner4@wisc.edu
Updated February 28, 2009
http://www.gen677.weebly.com