CD4 (ENSP00000011653) Background As part of the immune system, these cells help out by tagging pathogens or other unrecognizable objects to be targeted by other cells such as phagocytes. They are found on the outside of immune cells as glycoproteins.
Methods To obtain the predicted whale shark protein sequence, the human protein sequence for CD4 (ENS00000011653) was first obtained through the Ensemble website. It was then blasted against the predicted whale shark protein sequence using galaxy through the Georgia aquarium website. Reciprocal blasts were then conducted from the top hits of the predicted whale shark sequences on the human genome to see if the results would be the same or similar. The data was then used to further predict the whether or not protein sequences were orthologous.
Searching for CD4 in the whale shark
The human CD4 protein sequence was used to blast against the predicted whale shark sequence via galaxy from the Georgia aquarium website. Table 1 shows the top five results from the protein blast.
Whale Shark ID
E-value
Aligment
Protein Length
%identity
gi38197737
0
458
697
100
gi10835167
0
458
458
100
gi179144
0
458
458
99.78
gi675757545
0
458
458
99.34
gi161075433
0
458
458
99.34
Table 1: The top five results from the blast using the predicted protein sequence from galaxy. The top results came from those with the lowest e-value, though there were more results following with e-values at zero as well. Along side the e-values, the table gives the whale shark database ID, their alignment length, their protein length, and their percent identity. The sequences given where then used in a reciprocal blast against the human genome, each having results that with the top two hits having e-values of 0 and a third close to e^-130. The percent identities were then either 99 or 100%.
Protein Domain Immunoglobulin- All the top hits from the predicted whale shark protein have the protein domain Immunoglobulin, though the Whale Shark ID gi38197737 also has a GFP superfamily and T-cell superfamily that the other four do not (figure 1).
CD search result summary
Figure1. Whale Shark ID gi38197737 blasted against the human protein sequence giving a common domain, yet being the only one to have a T-cell and GFP superfamily.
Image obtained via- http://blast.ncbi.nlm.nih.gov/Blast.cgi
The rest of the top hits lacked both the Tcell and GFP superfamilies (figure 2).
CD search result summary
Figure2. The rest of the top hits botained from galaxy gave the following results when blasted against the human protein sequence.
Image obtained via- http://blast.ncbi.nlm.nih.gov/Blast.cgi Immunoglobulins work alongside antibodies to help fight against pathogens. Though both are essentially used as markers, the differ in what they are marking; for example, the function of a pathogen will be marked by antibodies while immunoblobulins will mark the structure.
Orthologs The protein sequence for human CD4 was blasted against the sequences for guinea pigs, chickens, honey bees, and yeast. Of the 4 species blasted, only two appear to be orthologs. For the guinea pig result, they appear to have a similar glycoprotein found on their immune cells, while chickens appear to have a differing variation that may be similar; however, for the honeybee and yeast blasts the the results came back with different proteins. for the yeast it was a transcription factor and for the honeybee it appeared to be a membrane-specific proteoglycan.
Forkhead family transcription factor FKH1 [Saccharomyces cerevisiae S288c]
484
NP 012135.1
0.80
Table2. The table shows the results of the best blast results from http://blast.ncbi.nlm.nih.gov/Blast.cgi hits for guinea pigs, chickens, honey bees, and yeast. The only significant one being that from the guinea pig as the other e-values are too high.
Phylogenetic tree The phylogenetic tree shows that the protein sequence for whale sharks and humans, for the protein CD4, have a more recent common ancestor than the rest. The results then show guinea pigs having the next most recent common ancestor, followed by chickens, honey bees, and lastly yeast.
Conclusion Researching the CD4 protein within other organisms such as whale sharks, guinea pigs, chickens, yeast, and honey bees leads to similar results to that of humans within whale sharks, chickens and guinea pigs. For the whale sharks, it can be concluded that the proteins are orthologs seeing as how closely similar they were from the blast and reciprocal blasts. They also had nearly identical alignments with little variation between them.
Background
As part of the immune system, these cells help out by tagging pathogens or other unrecognizable objects to be targeted by other cells such as phagocytes. They are found on the outside of immune cells as glycoproteins.
Methods
To obtain the predicted whale shark protein sequence, the human protein sequence for CD4 (ENS00000011653) was first obtained through the Ensemble website. It was then blasted against the predicted whale shark protein sequence using galaxy through the Georgia aquarium website. Reciprocal blasts were then conducted from the top hits of the predicted whale shark sequences on the human genome to see if the results would be the same or similar. The data was then used to further predict the whether or not protein sequences were orthologous.
Searching for CD4 in the whale shark
The human CD4 protein sequence was used to blast against the predicted whale shark sequence via galaxy from the Georgia aquarium website. Table 1 shows the top five results from the protein blast.Protein Domain
Immunoglobulin- All the top hits from the predicted whale shark protein have the protein domain Immunoglobulin, though the Whale Shark ID gi38197737 also has a GFP superfamily and T-cell superfamily that the other four do not (figure 1).
Figure1. Whale Shark ID gi38197737 blasted against the human protein sequence giving a common domain, yet being the only one to have a T-cell and GFP superfamily.
Image obtained via- http://blast.ncbi.nlm.nih.gov/Blast.cgi
The rest of the top hits lacked both the Tcell and GFP superfamilies (figure 2).
Figure2. The rest of the top hits botained from galaxy gave the following results when blasted against the human protein sequence.
Image obtained via- http://blast.ncbi.nlm.nih.gov/Blast.cgi
Immunoglobulins work alongside antibodies to help fight against pathogens. Though both are essentially used as markers, the differ in what they are marking; for example, the function of a pathogen will be marked by antibodies while immunoblobulins will mark the structure.
Orthologs
The protein sequence for human CD4 was blasted against the sequences for guinea pigs, chickens, honey bees, and yeast. Of the 4 species blasted, only two appear to be orthologs. For the guinea pig result, they appear to have a similar glycoprotein found on their immune cells, while chickens appear to have a differing variation that may be similar; however, for the honeybee and yeast blasts the the results came back with different proteins. for the yeast it was a transcription factor and for the honeybee it appeared to be a membrane-specific proteoglycan.
Phylogenetic tree
The phylogenetic tree shows that the protein sequence for whale sharks and humans, for the protein CD4, have a more recent common ancestor than the rest. The results then show guinea pigs having the next most recent common ancestor, followed by chickens, honey bees, and lastly yeast.
Conclusion
Researching the CD4 protein within other organisms such as whale sharks, guinea pigs, chickens, yeast, and honey bees leads to similar results to that of humans within whale sharks, chickens and guinea pigs. For the whale sharks, it can be concluded that the proteins are orthologs seeing as how closely similar they were from the blast and reciprocal blasts. They also had nearly identical alignments with little variation between them.
References
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome
http://useast.ensembl.org/index.html
http://whaleshark.georgiaaquarium.org/
http://www.ebi.ac.uk/Tools/msa/clustalw2/
Immunoglobulins: Structure and functions. (2009, May 25). Retrieved from https://biochemistryquestions.wordpress.com/2009/05/26/immunoglobulins-structure-and-functions/
T-cell surface glycoprotein CD4. (n.d.). Retrieved from http://www.uniprot.org/uniprot/P01730
CD4 Gene. (n.d.). Retrieved from http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD4