What is Gene Ontology (GO)? [1]
Gene ontology provides defined terms for gene product properties. GO is structured so terms have defined relationships to one or more other terms in the same domain, and sometimes to other domains. This information can be useful when attempting to locate the function and location of a gene. The GO vocabulary is designed to be species-neutral and includes terms applicable to prokaryotes and eukaryotes. Gene Ontology highlights three key aspects of the gene:
Cellular Component:
Component of a cell (also known as an organelle) that is related to the gene of interest. Examples of such cellular components include: lysosome, vacuole, ribosomes, etc. This information is useful to locate the gene of interest. |
Molecular Function:
Molecular function describes activities, such as catalytic or binding activities, that occur at the molecular level. Molecular functions generally correspond to activities that can be performed by individual gene products, but some activities are performed by assembled complexes of gene products. |
Biological Process:
A biological process is a series of events accomplished by one or more ordered assemblies of molecular functions. It can be difficult to distinguish between a biological process and a molecular function, but the general rule is that a process must have more than one distinct step. |
What are the GO terms of CLN3? [2]
Cellular Component
CLN3 is a transmembrane protein located in the plasma membrane of neuronal vacuoles and lysosomes. It contains one transmembrane domain. Lysosomes are used in neurons to break down cellular waste and transport the waste from the cell. |
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CLN3 Gene Interactions:
The conserved protein interactions give insight into the function of the CLN3 protein. For example, CLN3 protein's direct interactions with other proteins involved in golgi-mediated transport, and lysosome organization suggest that the CLN3 protein first resides in the Golgi then moves to the lysosome via expelled vesicles. The direct interaction with RNA binding proteins suggest that the CLN3 protein could be involved in translation, or posttranslational modifications.
Conclusion:
Gene ontology is essential to discover and understand the function of CLN3, as well as its role in Batten Disease. Beginning with where the protein is located, can guide researchers to find more information about the protein's potential function. For example, knowing the lysosome is involved in cellular waste validates intuition of researchers to believe that CLN3 is involved in metabolizing cellular waste. Understanding that CLN3 is also a transmembrane protein, one can hypothesize that CLN3 is more specifically involved in transport of cellular waste into the lumen of the lysosome. This cannot be assumed, however, and more research must be conducted to fully understand its function.
References
[1] Gene Ontology. (n.d.). An Introduction to the Gene Ontology. <ftp://ftp.geneontology.org/go/www/GO.doc.shtml>
[2] Somogyi, A., Petcherski, A., Beckert, B., Huebecker, M., Priestman, D., Banning, A., . . . Tikkanen, R. (2018). Altered Expression of Ganglioside Metabolizing Enzymes Results in GM3 Ganglioside Accumulation in Cerebellar Cells of a Mouse Model of Juvenile Neuronal Ceroid Lipofuscinosis. International Journal of Molecular Sciences,19(2), 625. doi:10.3390/ijms19020625
Header: https://geneticliteracyproject.org/2016/08/26/scientists-can-now-guide-crispr-gene-editing-light/
Figure 1: https://www.studyread.com/importance-of-lysosomes/
Figure 2: https://www.researchgate.net/figure/13-CLN3-topology-and-juvenile-onset-neuronal-ceroid-lipofuscinosis-mutations-The_fig2_315715625
Figure 3: https://www.researchgate.net/figure/CLN3-and-sphingolipid-signaling-pathway-interactions-analyzed-using-Pathway-Studio_fig4_283492698
[2] Somogyi, A., Petcherski, A., Beckert, B., Huebecker, M., Priestman, D., Banning, A., . . . Tikkanen, R. (2018). Altered Expression of Ganglioside Metabolizing Enzymes Results in GM3 Ganglioside Accumulation in Cerebellar Cells of a Mouse Model of Juvenile Neuronal Ceroid Lipofuscinosis. International Journal of Molecular Sciences,19(2), 625. doi:10.3390/ijms19020625
Header: https://geneticliteracyproject.org/2016/08/26/scientists-can-now-guide-crispr-gene-editing-light/
Figure 1: https://www.studyread.com/importance-of-lysosomes/
Figure 2: https://www.researchgate.net/figure/13-CLN3-topology-and-juvenile-onset-neuronal-ceroid-lipofuscinosis-mutations-The_fig2_315715625
Figure 3: https://www.researchgate.net/figure/CLN3-and-sphingolipid-signaling-pathway-interactions-analyzed-using-Pathway-Studio_fig4_283492698
This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.