Matthew Loper: M13 Renovation

M13

Gene	Current Function	Potential Re-Engineering Ideas
1	Assembly	It would be interesting to test how much p1, p4, and p11 depend on each other. Is it possible to modify one gene without disrupting the function of the other two? I would also like to vary the number of secretion channels to test whether increasing the number of channels decreases the length of the phage's life cycle.
2	+ strand DNA replication	Again, this gene overlaps with another gene with a different function (gene 10). It may be useful to seperate p2 and p10 so that they can be changed independently. Perhaps we could make + strand replication faster
3	phage tail protein which is initial point of infection	Increase binding affinity so that in a population of bacteria there is a higher rate of M13 infection
4	Assembly	Similar function to p1
5	Binds ssDNA/make protein DNA complexes	Again, I see potential to decrease the phage life cycle/create greater efficiency. Altering p5 could increase the rate of replication
6	phage tail protein	This tail protein does not seem to be as necessary to the infection process as p3 so it may be a convenient location to add a GFP fusion for labelling purposes.
7	phage head protein	If GFP fusion on p6 was not successful this is another good candidate for labeling purposes.
8	Phage coat protein (2700 copies)	Currently flexible in order to adjust size to genome size. Modify rigidity in order to essentially cap genome size at desired modified size as a check on inadvertent modifications and mutations.
9	Blunt end of phage	Make this gene like p3...can we change side selectivity of M13? Would M13 be able to infect using both ends? How would this affect the virus?
10	+ strand accumulation	Modulate from p2. Can we increase strand accumulation in host? How does this affect replication rate?
11	Assembly	Same as p1