Adenylyl Cyclase Orthologs
This web page was produced as an assignment for an undergraduate course at Davidson College.
Orthologs
Orthologs are genes in different species that have evolved from a common gene. The differences in the orthologs depend on when the species separated during evolution. Specific amino acids tend to be conserved in many species because they are essential to the proper function of the protein. However, it should not be a surprise that the Homo sapiens gene of adenylyl cyclase type VIII shares more conserved sequences with the Pan troglodytes (chimpanzee) than it does with the Drosophila melanogaster (fruit fly) because of the closer relation during evolution.
Table 1. Adenylyl cyclase type VIII orthologs. This table provides details on six different orthologs of Homo sapiens adenylyl cyclase type VIII. (Image from http://genome-www.stanford.edu/genecards/index.shtml 2005)
This table shows the similarity of the human adenylyl cyclase type VIII gene, which is 1251 amino acids longs, to the comparable genes in the Pan troglodytes, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, and Anopheles gamibae. The first row indicates that the chimpanzee has a nucleotide sequence that is 99.18 percent the same as the human sequence and 100 percent the same in the amino acid sequence. This difference between the two percentages could be attributed to a silent mutation of a nucleotide that did not alter the encoded amino acid. However, the similarity between the human and Drosophila melanogaster is only 51.99 percent for the nucleotide sequence and 42.36 percent for the amino acid sequence (GeneCards 2005). This reaffirms that the separation of these species occurred earlier than the separation of the human and the chimpanzee in the theory of evolution.
Specifically in the orthologs of the human and chimpanzee genes, the sequences of these genes have a region of 162 identical amino acids. The sequences were found using the gene database of the NCBI web site (NCBI 2005). Although the sequence of amino acids is much smaller for the chimpanzee, the exact sequence of 162 amino acids listed are also found within the amino acid sequence of humans, as seen here in the green highlighter. It is not clear why only 162 amino acids are listed in this sequence, but in the following figure it is easier to see the high amount of identical sequence between the chimpanzee and human sequences.
Figure 1. Comparison of part of the Human and Chimpanzee gene sequences of adenylyl cyclase type VIII. This figure demonstrates the close similarities between the human and chimpanzee gene sequences. (Image from www.ensembl.org 2005)
The rat ortholog, which is 1248 amino acids long, has a similar sequence to both the chimpanzee and human sequences, but has a mutation at the amino acid 487 of its listed amino acid sequence (as seen in blue in in this sequence). The mutation differs in the tyrosine of the chimpanzee and human amino acid sequences changed to a phenylalanine in the rat sequence. This is a change from a polar hydrophobic amino acid to a nonpolar, hydrophilic amino acid, which may affect the shape of the protein. There are other differences between the rat and human sequences, some of which have changes as mentioned here and others that no not change in its polarity or affinity for water. It seems as though, however, the start sequences and the termination sequences have remained in tact so that the protein will definitely be made. Nevertheless, if the if the mutations change the shape of a g-protein receptor site, the protein may not be able to function correctly. It is more likely that many of these mutations do not cause an nonfunctioning protein because evolution chooses the proteins that will be able to function to survive. The following figure shows an easier way to see that when the two sequences are aligned, there are many sections that are similar, but there are also some gaps that do not align.
Figure 2. Comparison of part of the Human and Rat gene sequences of adenylyl cyclase type VIII. This figure demonstrates the similarities between the human and rat gene sequences, but also reveals more gaps and stretches between the two sequences. (Image from www.ensembl.org 2005)
The sequence of the mouse gene for adenylyl cyclase type VIII, which is 1249 amino acids and can be found here, was found in the NCBI database to be very similar to that of the rat ortholog sequence, which is supported by figure 1 (NCBI 2005). Both the rat and mouse orthologs have about 90 percent of their nucleotides similar with those of the human nucleotide sequence and about 97 percent of the amino acid sequences similar to that of the human sequence (GeneCards 2005). The alignment of the mouse gene sequence and the human gene sequence also yield a similar result to that of the alignment of the rat and human genes.
Figure 3. Comparison of part of the Human and Mouse gene sequences of adenylyl cyclase type VIII. This figure demonstrates the similarities between the human and mouse gene sequences, which is very similar to the figure comparing the human and rat sequences. (Image from www.ensembl.org 2005)
The Drosophila melanogaster sequence for the adenylyl cyclase type VIII gene was also unable to be found in the NCBI database, but the NCBI used the gene sequence for the Drosophila adenylyl cyclase 78C, which is 1694 amino acids long and can be found here (NCBI 2005). Table 1, as seen above, reveals that only about 52 percent of the nucleotide sequence is similar to the human sequence and about 42 percent of the amino acid sequence is similar to that of a human's (GeneCards 2005). The gene sequence of Drosphila was not identically lined up with the sequence of humans. There are four main sequences that line up, but they do not run continuously through the gene sequence as seen in the figure below (NCBI 2005).
Figure 4. Blast 2 Sequences results for Homo sapiens against Drosophila melanogaster . This figure shows that there are some similar sections of the Drosophila and human gene sequences, but they are not continuous. (Image from www.ncbi.nlm.nih.gov 2004)
Unfortunately, the HomoloGene database was unable to find any sequences for the organisms Saccharomyces cerevisiae, Arabidopsis thaliana, or Pinus teada that had a similarity to the human adenylyl cyclase type VIII. (GeneCards 2005)
Mutations
As mentioned previously, some species only vary in gene sequences by a few mutations. However, these mutations can have huge effects on the function of the protein. For example, some mutations may slightly change the shape of the binding site and make a protein have a higher affinity for binding with its substrate than it had before the mutation. In the case of Parkinson's Disease, the amount of activity of the dopamine-stimulated adenylyl cyclase is very high. This may be a result of increased levels of dopamine or of a higher binding affinity of the adenylyl cyclase to the dopamine. Either way the result is tragic, and if it is a possible cause of Parkinson's Disease, it should be looked into further (Tong et al. 2004).
Not only can a mutation increase the activity of a protein, it can also decrease or halt the activity of the protein. If a mutation changes the overall shape of a protein, the protein may not be able to function. this could cause major problems for the pathways and other proteins that depend on the mutated protein. Adenylyl cyclase type VIII is unique because it has a long carboxyl terminus and a long amino terminus that seem to be involved in learning, memory, and drug dependence. If the shape of this protein is changed too much, the protein may not be able to function all or will show a decrease in function, which in turn would probably cause a decrease in learning and in memory and an increase in drug dependence (Defer et al. 1994).
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References:
NCBI. 2005. <http://www.ncbi.nlm.nih.gov/> Accessed 8 March 2005.
GeneCards Homepage. 11 Jan. 2005. Xennex, Inc.. 24 Jan. 2005 <http://genome-www.stanford.edu/genecards/index.shtml>. Accessed 8 March 2005
"project Ensembl." Ensembl Genome Browser. The Wellcome Trust Sanger Institute. <http://www.ensembl.org/>. Accessed 8 Mar 2005.
Defer, N., O. Marinx, D. Stengel, and A. Danisova. "Molecular cloning of the human type VIII adenylyl cyclase." FEBS Letters 351.1 (1994): 109-113.
Tong, J., P. S. Fitzmaurice, A. C. Ang, and Y. Furukawa. "Brain dopamine-stimulated adenylyl cyclase activity in Parkinson's disease, multiple system atrophy, and progressive supranuclear palsy." Annals of Neurology 55.1 (2003): 125-129.