This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison
Homology
In 1848, Richard Owen coined the term "homology" to define the physical similarities of organisms [1]. Homologous structures indicate a common evolutionary ancestor. An example of homology is the forelimb of tetrapods. Frogs, rabbits, lizards, and birds have forelimbs with different functions, but these forelimbs all contain the same bones--bones that were unearthed in a fossil of an extinct common ancestor [2]. Like physical features such as appendages, DNA homology can also be used to determine the probability of two genes sharing a common ancestor [3]. However, there is one caveat. One must be wary of analogs. Analogous sequences or physical similarities can result from convergent evolution or chance [3].
The homologs of the PER2 protein were determined using the National Center for Biotechnology Information (NCBI)'s program, BLAST. Basic Local Alignment Search tool, or BLAST allows one to enter the FASTA sequence of DNA, mRNA, or protein. BLAST uses a database to compare these sequences, identifying similarities and identical sequences in other organisms. The larger the percent of similarity, the lower the probability that these sequences are similar due to convergent evolution or chance [4]. BLAST indicated quite a few homologs (see below). These results were confirmed using Homolgene. Please note that the list of homologs (below) is not extensive, but rather one containing the homologs with the most similar sequences and homologs in model organisms often used in genetic research.
The homologs of the PER2 protein were determined using the National Center for Biotechnology Information (NCBI)'s program, BLAST. Basic Local Alignment Search tool, or BLAST allows one to enter the FASTA sequence of DNA, mRNA, or protein. BLAST uses a database to compare these sequences, identifying similarities and identical sequences in other organisms. The larger the percent of similarity, the lower the probability that these sequences are similar due to convergent evolution or chance [4]. BLAST indicated quite a few homologs (see below). These results were confirmed using Homolgene. Please note that the list of homologs (below) is not extensive, but rather one containing the homologs with the most similar sequences and homologs in model organisms often used in genetic research.
PER2 Protein Homologs
Human (Homo sapiens):
period circadian protein homolog 2 [Homo Sapiens] Accession number: NP_073728 GI Number: 12707562 FASTA |
Fruit Fly (Drosophila pseudoobscura):
per protein Accession number: CAA32082.1 GI Number: 9076 FASTA E Value: 6e-3 Max Identical: 29% % Similar: 46% |
Chimpanzee (Pan troglodytes):
period circadian protein homolog 2 isoform 2 [Pan troglodytes] Accession number: XP_001154734.2 GI Number: 332815837 FASTA E Value: 0.0 Max Identical: 91% % Similar: 91% |
Rhesus Monkey (Macaca mulatta):
PREDICTED: period circadian protein homolog 2 [Macaca mulatta] Accession number: XP_001086845.2 GI Number: 297265213 FASTA E Value: 0.0 Max Identical: 93% % Similar: 94% |
Dog (Canis lupis familiaris):
PREDICTED: period circadian protein homolog 2 isoform X1 [Canis lupus familiaris] Accession number: XP_005635982.1 GI Number: 545543068 FASTA E Value: 0.0 Max Identical: 73% % Similar: 80% |
Cattle (Bos taurus):
period circadian protein homolog 2 [Bos taurus] Accession number: NP_001179246.1 GI Number: 300796796 FASTA E Value: 0.0 Max Identical: 73% % Similar: 80% |
House Mouse (Mus musculus):
period homolog 2 (Drosophila) [Mus musculus] Accession number: EDL40029.1 GI Number: 148708082 FASTA E Value: 0.0 Max Identical: 77% % Similar: 83% Red Jungle Fowl (Gallus gallus):
period circadian protein homolog 2 [Gallus gallus] Accession number: NP_989593.1 GI Number: 45383610 FASTA E Value: 0.0 Max Identical: 58% % Similar: 70% |
Brown Rat (Rattus norvegicus):
period circadian protein homolog 2 [Rattus norvegicus] Accession number: NP_113866.1 GI Number: 13928942 FASTA E Value: 0.0 Max Identical: 77% % Similar: 84% Zebrafish (Danio rerio):
Per2 protein [Danio rerio] Accession number: AAI63549.1 GI Number: 190337630 FASTA E Value: 0.0 Max Identical: 51% % Similar: 64% |
Western Lowland Gorilla (Gorilla gorilla gorilla):
PREDICTED: period circadian protein homolog 2 [Gorilla gorilla gorilla] Accession number: XP_004033482.1 GI Number: 426339059 FASTA E Value: 0.0 Max Identical: 99% % Similar: 99% |
Deer Tick (Ixodes scapularis):
period circadian protein, putative [Ixodes scapularis] Accession number: XP_002410891.1 GI Number: 241173807 FASTA E Value: 2e-39 Max Identical: 31% % Similar: 47% |
African Clawed Frog (Xenopus laevis):
period circadian clock 1 [Xenopus laevis] Accession number: NP_001079172.2 GI Number: 308522714 FASTA E Value: 0.0 Max Identical: 42% % Similar: 55% |
Blind Cave Fish (Astyanax mexicanus): period 2, partial
Accession number: AHA91703 GI Number: 558850325 FASTA E Value: 5e-81 Max Identical: 72% % Similar: 84% |
Analysis
As you can see from this list of homologs, the PER2 protein is highly conserved among the animal kingdom. This homology reflects the importance of the PER2 gene and its protein. Since PER2 regulates the circadian rhythm, an essential cycle in living organisms, this is not surprising. Primate PER2 proteins are most identical to the human protein, surprisingly followed by the blind cavefish, then other mammals, fowl, fish and an amphibian, and lastly, insects. Explore the phylogeny page for more information on these homologs relationships.
References
[1] Evolution Makes Sense of Homologies. http://www.zoology.ubc.ca/~bio336/bio336/lectures/lecture5/overheads.html
[2] Understanding Evolution. Homologies.
[3] Schope, Thomas. (1983). Homology. Science,219 (4582). http://www.jstor.org/stable/1690261
[4] Koonin, E.V. and Gaperin, M.Y. Sequence-Evolution-Function: Computational Approaches in Comparative Genomics. Boston: Kluwer Academic; 2003. Chapter 2, Evolutionary Concept in Genetics and Genomics. Available from http://www.ncbi.nlm.nih.gov/books/NBK20255/
[1] Evolution Makes Sense of Homologies. http://www.zoology.ubc.ca/~bio336/bio336/lectures/lecture5/overheads.html
[2] Understanding Evolution. Homologies.
[3] Schope, Thomas. (1983). Homology. Science,219 (4582). http://www.jstor.org/stable/1690261
[4] Koonin, E.V. and Gaperin, M.Y. Sequence-Evolution-Function: Computational Approaches in Comparative Genomics. Boston: Kluwer Academic; 2003. Chapter 2, Evolutionary Concept in Genetics and Genomics. Available from http://www.ncbi.nlm.nih.gov/books/NBK20255/