Assignment:
Question 1
The protein Transmembrane Serine Protease 2 (TMPRSS2) has been implicated in the SARS-CoV-2 infection mechanism. Use the review by Thunders and Delahunt (2020, URL below) to help you answer the following questions.
(a) Using the NCBI protein database (or any other interweb resource of your choice), find the protein sequence of TMPRSS2 isoform 2 and paste it below.
(b) What is the sequence of the TMPRSS2 isoform 2 transmembrane domain?
(c) Using the EMBL EMBOSS web server, determine the hydropathy plot for this protein and copy/paste a time-stamped plot below.
(d) Highlight the transmembrane domain on the hydropathy plot. Hint: look at the accompanying reference(s) to help you home in on the region.
(e) Which end of TMPRSS2 (N or C-terminus) is oriented toward the cytoplasm?
(f) In theory, TMPRSS2 could insert into the membrane in either direction (N-terminus to the ER lumen, or N-terminus to the cytoplasm). What amino acids in the primary sequence of TMPRSS2 help set this orientation? Refer to your lecture notes if you're not sure.
(g) What is the TMPRSS2 endoplasmic reticulum (ER) trafficking signal? Hint: the webtool SignalP(URL below) is quite good at predicting N-terminal signals but not internal signals.
(h) Where in the cell is TMPRSS2 localized? Here's another useful tool to help you...
(i) Using your carefully curated Cell Biology lecture notes as a guide, write a paragraph summarizing how TMPRSS2 is trafficked to its final location in the cell. Include a diagram to illustrate this path.
Question 2
For the SARS-CoV-2 virus to actually invade a cell, it must somehow fuse its viral membrane coat with the plasma membrane. Two pathways have been established, one "early" and one "late". Using the accompanying Millet and Whittaker (2018) paper as your guide (see URL below), answer the following questions. Note: the Millet and Whittaker paper reviews SARS-CoV, but the biology behind cellular invasion for SARS-CoV and SARS-CoV-2 should be similar.
(a) What organelles are utilized in the viral "late" invasion pathway?
(b) Write a paragraph explaining how the virus gains access to the cytoplasm via the "late" pathway. Include diagram(s) with your answer.
(c) Include one or more references in APA style that support your answer. Ensure that a Digital Object Identifier (DOI) number is included. If it magically links to the reference webpage then that will make me very happy.
(d) Do you think the virus needs to gain access to the nucleus to complete its replication cycle?
(e) Explain your answer to 2(d).
Readings:
1. Gene of the month: TMPRSS2 (transmembrane serine protease 2)
By Michelle Thunders , Brett Delahunt
2. Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells
By Jean Kaoru Millet, Gary R. Whittaker