Non: Week 14
Purpose
The purpose of this week's lab was to research the relationship between SARS-CoV-1/SARS-CoV-2 and the ACE2 receptor of different species. Specifically, our group chose to study a random assortment of primates because of their close relationship to humans.
Combined Methods/Results
We settled on analyzing the structure and function relationship between the ACE2 receptors of primates and SARS-CoV-2 (and SARS-CoV-1 for additional background). We chose primates at random, as long as they had a ACE2 receptor gene. The fifteen we chose were:
- Pongo abelii (Sumatran orangutan)
- Macaca nemestrina (Southern pig-tailed macaque)
- Pan troglodytes (Chimpanzee)
- Tarsius syrichta (Philippine tarsier)
- Nomascus leucogenys (Northern white-cheeked gibbon)
- Propithecus coquereli (Coquerel's sifaka)
- Chlorocebus sabaeus (Green monkey)
- Saimiri boliviensis boliviensis (Black-capped squirrel monkey)
- Macaca fascicularis (Crab-eating macaque)
- Aotus nancymaae (Nancy Ma's night monkey)
- Pan paniscus (Bonobo)
- Rhinopithecus bieti (Black snub-nosed monkey)
- Papio anubis (Olive baboon)
- Macaca mulatta (Rhesus macaque)
- Rhinopithecus roxellana (Golden snub-nosed monkey)
I specifically worked on sequence analysis of the fifteen primates and human ACE2.
- I clustally aligned on phylogeny.fr the sixteen sequences (15 primates + homo sapiens) and imported them into Excel.
- I highlighted amino acid residues based on their polarity.
- I determined the consensus between the 16 sequences and calculated the percentage of residues that corresponded with the consensus.
- I looked at 12 amino acid residue locations identified by Melin et al. (2020) that were deemed important to SARS-CoV-2 binding to ACE2 in humans.
- I calculated the number of residues that were conserved/semi-conserved/non-conserved at these 12 locations for each of the primates. This chart can be seen in the final presentation.
Data/Files
- Excel Spreadsheet of Sequence Analysis
- Clustally Aligned FASTA sequences document
- Final Presentation Powerpoint
- Final Presentation Google Slides Link
Scientific Conclusion
We found that many primates would be susceptible to SARS-CoV-2 based on their ACE2 sequence similarity to humans. These primates shared the same binding residues in the ACE2 receptor that allow for SARS-CoV-2 to enter the cell.
Acknowledgements
- I worked with my partners Jenny and Carolyn to research and create presentation.
- I used the Week 14 Protocol for this assignment.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Non (talk) 23:14, 29 April 2020 (PDT)
References
- Melin, A. D., Janiak, M. C., Marrone, F., Arora, P. S., & Higham, J. P. (2020). Comparative ACE2 variation and primate COVID-19 risk. bioRxiv.
- OpenWetWare (2020). BIOL368/20:Week 14. Retrieved April 23, 2020 from https://openwetware.org/wiki/BIOL368/S20:Week_14.
- Phylogeny.fr. (2020) Phylogeny.fr:Home. Retrieved April 27, 2020, from http://www.phylogeny.fr/.
- UniProt (2020). UniProtKB results "ace2". Retrieved April 23, 2020 from https://www.uniprot.org/uniprot/?query=ace2&sort=score.
