The physical interaction with ERAP2 changes the basic enzymatic parameters of ERAP1 and improves its substrate-binding affinity (Evnouchidou et al.). The major histocompatibility complex (MHC) class I molecules rely on aminopeptidases such as ERAP1 (Tanioka et al., 2003).These aminopeptidases hydrolyze N-terminal amino acids of proteins or peptide substrates and play a central role in peptide trimming which is a step required for the generation of most HLA class I-binding peptides. ERAP2 is highly expressed in spleen and leukocytes (UniProt).
Figure 1. Endoplasmic reticulum aminopeptidase 2 plays a central role in peptide trimming. Once trimmed, these peptides play a large role on the cell membrane in expression and export.
Methods
Whaleshark Predicted Orthologs The human protein sequence (ENSP00000400376) was used as the query in a Blast. This query was placed against the predicted whale shark protein database which was found in the whaleshark.georgiaaquarium.org Galaxy server. The top 5 predicted protein hits were used as queries in protein BLASTs against the NCBI human protein database.
Predicted Orthologs ERAP2 predicted orthologs were identified in species other than whale sharks using the NCBI Blast serves. Protein BLASTs were performed using single species protein databases for zebrafish, mouse, elephant shark, elephat, yeast, and rabbit.
. Phylogenetic tree
The hit with the lowest E-value for each non-whale shark species search (using the human protein as query) along with the top 4 whale shark BLAST hits were used to create a multiple sequence alignment and phylogenetic tree. ClustalW2 with default settings was used to create the alignment and tree.
Table 1.Human ERAP 2 gene best hits in the Whaleshark Genome. These 6 hits had the lowest e-values and therefore were deemed the
closest matches contained within the whaleshark genome.4
The percent ID of the top match seems to evidence a close match between the top hit and the human ERAP 2 gene, but the e-value of this hit is moderately high (far away from zero). Also, when blasted back against the human genome, the top whale shark hit produces a human gene moderately similar to ERAP2, but not homologous. Therefore a bootstrapping technique was used in an attempt to get better results.
Bootstrapping:
Human ERAP2 gene is blasted against an organism more similar to the whale shark, like the elephant shark. The top hit from this blast is then blasted against the whale shark genome to see if results change.
Table 2. Shows the best hit for the human ERAP2 gene in the Elephant Shark genome.
This best hit shown above was then blasted against the whaleshark database to see if better results (e-values) would be obtained.
Sequence ID
E-value
% ID
Alignment Length
Query Coverage
g34464.t1
9e-24
80.77%
52
91
g29177.t1
3e-23
76.67%
60
97
Table 3. Exhibits the best hits of the elephant shark ERAP2 gene when blasted on the whale shark genome.
These two best hits were also the top two when the human ERAP2 gene was blasted on the whale shark genome. In comparison between the two, the elephant shark actually gave worse values for the best hit gene g34464.t1, but gave better values for the gene g29177.t1.
Conserved Domain:
Figure 2. Conserved domains in the ERAP2 gene.
Phylogenetic Tree:
Orthologues
Organism
Protein
E-value
query coverage (%)
% ID
Mouse
ERAP1
0.0
94.30
51.22
Zebrafish
ERAP2
0.0
95.00
58.46
Rabbit
ERAP1
0.0
94.56
53.32
Elephant
ERAP2
0.0
99.68
80.36
Yeast
APE2
3e-128
94.26
30.75
Table 4. Human ERAP2 gene blasted against other organisms to get values for comparison in a phylogenetic tree. Values in table are best hits for each organism.
Figure 3. A tree diagram of all the organisms best hits against the human ERAP2 gene highlights similarities between organisms.
Conclusion:
Finding best hits for the ERAP2 gene in the whale shark genome confirmed that the whale shark may have a similar gene to that of the human ERAP2 gene; however, when blasted back against the human genome, the results indicate that the whale shark gene g34464.t1 is not a homologue to ERAP2. This is further evidenced using bootstrapping techniques where the human ERAP2 gene was blasted against the elephant shark genome, which produced a homologous gene. This gene was then blasted against the whaleshark genome, but gave similar results to the human blast. It may be that the whale shark has genes that are distantly similar and produce proteins that perform distantly similar tasks, but are not homologous to ERAP2. The conclusion is that whale sharks do not have a homologous gene to ERAP2.
Works Cited: Evnouchidou, I., M. Weimershaus, L. Saveanu, and P. Van Endert. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 31 Mar. 2015.
"Endoplasmic Reticulum Aminopeptidase 2." ERAP2. UniProt, n.d. Web. 31 Mar. 2015. <http://www.uniprot.org/uniprot/Q6P179>. Tanioka, T., A. Hattori, S. Masuda, Y. Nomura, H. Nakayama, S. Mizutani, and M. Tsujimoto. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, 10 Jan. 2003. Web. 31 Mar. 2015. <http://www.ncbi.nlm.nih.gov/pubmed/12799365>.
ERAP2 (ENSP00000400376)
Background
The physical interaction with ERAP2 changes the basic enzymatic parameters of ERAP1 and improves its substrate-binding affinity (Evnouchidou et al.). The major histocompatibility complex (MHC) class I molecules rely on aminopeptidases such as ERAP1 (Tanioka et al., 2003).These aminopeptidases hydrolyze N-terminal amino acids of proteins or peptide substrates and play a central role in peptide trimming which is a step required for the generation of most HLA class I-binding peptides. ERAP2 is highly expressed in spleen and leukocytes (UniProt).Figure 1. Endoplasmic reticulum aminopeptidase 2 plays a central role in peptide trimming. Once trimmed, these peptides play a large role on the cell membrane in expression and export.
Methods
Whaleshark Predicted OrthologsThe human protein sequence (ENSP00000400376) was used as the query in a Blast. This query was placed against the predicted whale shark protein database which was found in the whaleshark.georgiaaquarium.org Galaxy server. The top 5 predicted protein hits were used as queries in protein BLASTs against the NCBI human protein database.
Predicted Orthologs
ERAP2 predicted orthologs were identified in species other than whale sharks using the NCBI Blast serves. Protein BLASTs were performed using single species protein databases for zebrafish, mouse, elephant shark, elephat, yeast, and rabbit.
.
Phylogenetic tree
The hit with the lowest E-value for each non-whale shark species search (using the human protein as query) along with the top 4 whale shark BLAST hits were used to create a multiple sequence alignment and phylogenetic tree. ClustalW2 with default settings was used to create the alignment and tree.
Table 1. Human ERAP 2 gene best hits in the Whaleshark Genome. These 6 hits had the lowest e-values and therefore were deemed the
closest matches contained within the whaleshark genome.4
The percent ID of the top match seems to evidence a close match between the top hit and the human ERAP 2 gene, but the e-value of this hit is moderately high (far away from zero). Also, when blasted back against the human genome, the top whale shark hit produces a human gene moderately similar to ERAP2, but not homologous. Therefore a bootstrapping technique was used in an attempt to get better results.
Bootstrapping:
Human ERAP2 gene is blasted against an organism more similar to the whale shark, like the elephant shark. The top hit from this blast is then blasted against the whale shark genome to see if results change.
Score
Score
Cover
Table 2. Shows the best hit for the human ERAP2 gene in the Elephant Shark genome.
This best hit shown above was then blasted against the whaleshark database to see if better results (e-values) would be obtained.
These two best hits were also the top two when the human ERAP2 gene was blasted on the whale shark genome. In comparison between the two, the elephant shark actually gave worse values for the best hit gene g34464.t1, but gave better values for the gene g29177.t1.
Conserved Domain:
Figure 2. Conserved domains in the ERAP2 gene.
Phylogenetic Tree:
Orthologues
Figure 3. A tree diagram of all the organisms best hits against the human ERAP2 gene highlights similarities between organisms.
Conclusion:
Finding best hits for the ERAP2 gene in the whale shark genome confirmed that the whale shark may have a similar gene to that of the human ERAP2 gene; however, when blasted back against the human genome, the results indicate that the whale shark gene g34464.t1 is not a homologue to ERAP2. This is further evidenced using bootstrapping techniques where the human ERAP2 gene was blasted against the elephant shark genome, which produced a homologous gene. This gene was then blasted against the whaleshark genome, but gave similar results to the human blast. It may be that the whale shark has genes that are distantly similar and produce proteins that perform distantly similar tasks, but are not homologous to ERAP2. The conclusion is that whale sharks do not have a homologous gene to ERAP2.
Works Cited:
Evnouchidou, I., M. Weimershaus, L. Saveanu, and P. Van Endert. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 31 Mar. 2015.
"Endoplasmic Reticulum Aminopeptidase 2." ERAP2. UniProt, n.d. Web. 31 Mar. 2015. <http://www.uniprot.org/uniprot/Q6P179>.
Tanioka, T., A. Hattori, S. Masuda, Y. Nomura, H. Nakayama, S. Mizutani, and M. Tsujimoto. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, 10 Jan. 2003. Web. 31 Mar. 2015. <http://www.ncbi.nlm.nih.gov/pubmed/12799365>.