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 should use a stronger promoter for p2 so that we may increase p2 activity to replicate more DNA.
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. We want p3 to bind better to the TolA protein of the bacterial pilus by increasing the affinity of p3 for TolA.
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. We can alter a few amino acids to see how the shape of p4 may change the ability of phage to exit the cell.
V	Binds ssDNA to package new phage, competes with p2, initial protein coat for ssDNA	We want to increase the number of ssDNA that p5 can bind to. We can do this by making base changes that
VI	Phage tail protein (cap)	p6 is buried under p3. Is the presence of p6 important for p3 to work? What if we silenced the start codon for p6?
VII	Phage head protein	p7 and p9 are both minor coat proteins. We could fuse these genes together and see whether the resulting protein works as well as p7 and p9.
VIII	major Phage coat protein, replaces p5 protein coat as phage is secreted	A lot of p8 is produced since it coats the entire surface of the phage. Could we induce the phage to produce more coat proteins like p9 than p7 and can they replace p8 without disturbing phage viability?
IX	Phage Head Protein, interacts with p7 protein and p5-ssDNA to start phage secretion	We could add a gfp tag at the N-terminus of this gene so that we can track the growth of phage and infection in real-time.
X	DNA replication; regulates # of dsDNA	Use a stronger ribosome binding site so that more p10 will be produced, allowing more + strands to accumulate in the host for packaging.
XI	Assembly, channel formation & exit	See description for g1. Alternatively, we can unstuff the sequence of g1 and g11 so that the genes are separated, and see whether this alteration affects phage assembly.

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).