Homology
Homology is quantifying the similarities of sequences or structures between organisms by looking at common ancestry[1]. Using homology can help find conserved sequences and structures that can be used to look at genes of interest.
Homo sapiens
ACCESSION #: NP_000040 |
Mus musculus
ACCESSION #: NP_075602 |
Danio rerio
ACCESSION#: NP_001103573 |
Xenopus tropicalis
ACCESSION#: Q28C61 |
Rattus norvegicus
|
There are five homologs for the ASPA gene, as shown above. ASPA is highly conserved in these species. Their information comes from PubMed and Homologene.
Phylogeny
Phylogeny is the study of historical and evolutionary relationships between animals by looking at the their DNA and protein sequences[2]. Phylogeny is represented through phylogenetic trees, which show branches that break off when splitting away into a new organism.
Maximum likelihood tree made with MegaX software
ASPA homologs show similar phylogeny in the maximum likelihood tree. All the model organisms are vertebrates, which makes sense as this gene has relation to the central nervous system.
Protein Domain
A protein domain is a part of the protein's structure. The gene can have multiple domains, as well as proteins have have domains that belong to multiple related genes[3].
Pfam protein domains found using SMART
ASPA has one domain, AstE_AspA. This domain's function is the break down of aspartoacylase into aspartate and acetate[4]. This domain is very well conserved throughout the homologs.
Protein Interaction Network
A protein interaction network is a union of all the proteins and the interactions between them[5]. These can be used to look at the interactions between a protein of interest and the related proteins. The interactions can be categorized by some of the proteins functions or processes that it is involved in.
Protein interaction networks were found for both humans and zebrafish ASPA genes. In humans, some of the interactions between proteins include metabolic processes, central nervous system development, and myelination. In the experimental model zebrafish, the interactions between proteins include aspartate metabolism and biosynthetic processes. These processes and functions align well with the gene ontology of ASPA.
References
[1] Koonin EV, Galperin MY. Boston: Kluwer Academic; 2003. www.ncbi.nlm.nih.gov/books/NBK20255/
[2] M. Charleston, "Phylogeny", Brenner's Encyclopedia of Genetics (Second Edition), Academic Press, 2013, 324-325, https://doi.org/10.1016/B978-0-12-374984-0.01160-8.
[3] Protein Domains, Motifs, and Folds in Protein Structure. (2021, January 3). Retrieved May 7, 2021, from https://bio.libretexts.org/@go/page/16427
[4] pfam.xfam.org/family/aste_aspa
[5] Alzate O, editor. Neuroproteomics. Boca Raton (FL): CRC Press/Taylor & Francis; 2010.
[6] String Database
[1] Koonin EV, Galperin MY. Boston: Kluwer Academic; 2003. www.ncbi.nlm.nih.gov/books/NBK20255/
[2] M. Charleston, "Phylogeny", Brenner's Encyclopedia of Genetics (Second Edition), Academic Press, 2013, 324-325, https://doi.org/10.1016/B978-0-12-374984-0.01160-8.
[3] Protein Domains, Motifs, and Folds in Protein Structure. (2021, January 3). Retrieved May 7, 2021, from https://bio.libretexts.org/@go/page/16427
[4] pfam.xfam.org/family/aste_aspa
[5] Alzate O, editor. Neuroproteomics. Boca Raton (FL): CRC Press/Taylor & Francis; 2010.
[6] String Database