Ying Chan: M13 Renovation

Protein	Function	Re-engineering Ideas
I	assembly, channel formation, exit	P1 shares similar functions with p11 and p4. Their gene sequences also overlap. So it may be possible to fuse the 3 genes to create a protein with combined functions.
II	Replicate DNA, nicks DNA to start replication of + strand	G10 is conveniently placed within g2, and both genes share similar functions. If we want to increase replication of DNA, we need to alter p2 (i.e. using a stronger promoter)
III	p3 forms Phage tail protein cap (along w/p6), binding	P3 is vital to the exit of phages and along with p6, are of the first proteins to contact the host. Phage infection rate may increase if p3 binds better to TolA protein of the bacterial pilus.
IV	assembly; forms(w/ p1 & p11) channels on bacterial membrane for phage secretion	10^12 of p4 forms a stable barrel thru which phage can be exported out of the cell. Altering the shape of p4 may change the rates in which phage can leave the cell and infect bacteria.
V	Binds ssDNA to package new phage, competes with p2, initial protein coat for ssDNA	Increase the number of ssDNA that complexes with p5 to increase production of phage.
VI	Phage tail protein (cap)
VII	Phage head protein	p7 and p9 are both minor coat proteins. What would happen if we fused the genes? Would they still be able to interact correctly with p5?
VIII	major Phage coat protein, replaces p5 protein coat as phage is secreted
IX	Phage Head Protein, interacts with p7 protein and p5-ssDNA to start phage secretion
X	DNA replication; regulates # of dsDNA	Alter p10 so that it will allow more + strands to accumulate in the host for packaging.
XI	Assembly, channel formation & exit

Nature often preserves functionally critical genomic elements, and evolutionary cousins can help us identify which genetic elements are disposable, which are interchangeable, and which are essential. Who are M13's closest evolutionary relatives and how do they differ from the phage you're working with?

M13's closest evolutionary relatives are the fd and f1 filamentous phages. They are a group of single-stranded, rod shaped bacteria that are lysogenic. fd and f1 differ from M13 in their major protein coat.

Register for an account at the Registry for Standard Biological Parts. This site is a clearing house for engineered biological parts that can be used as substrates for building. Look up part BBa_M1307 and write a response to the following criticism: "BBa_M1307 is not a standard biological part and does not belong in the registry."

M13K07 is not defined as a standard biological part because it is a composite of different parts; therefore, it is acts as a "device", which has several functions, rather than as a part (has one function).