Bernice:superM13

1.

Re-engineering the M13K07 Genome

Gene	Base Pairs	Overlaps(bp's)	Function	Suggested Changes
I	3196-4242	IV(4220-4242), XI(3916-4242)	assembly
II	8268-831	X(496-831)	replication of DNA+strand
III	1579-2853	BamHI(2220-2225)	phage tail protein (5 copies), N-terminus mediates host recognition and infection, C-terminus required for release from the host cell phage (the last part of phage in contact with host) and helps provide structural stability	* Simplify sequence encoding for C-terminus to only produce critical proteins, making room to add sequences to other parts of the genome
IV	4220-5500	I(4220-4242), XI(4220-4242)	assembly
V	843-1106		binds ssDNA	* Lower efficiency of gene V so that extra viral DNA will be produced, but not packaged into the phage. Therefore, it may be incorporated into the host genome.
VI	2856-3194		phage tail protein (5 copies)	* See gene III,
VII	1108-1209	IX(1207-1208)	phage head protein (5 copies)
VIII	1304-1522	IX(1302-1303)	phage coat protein (2700 copies)	* Add fluorescent tag to protein to make phage easier to image, * Modify protein to increaes affinity to a surface composed of a specific material. *
IX	1206-1304	VII(1207-1208), VIII(1302-1303)	phage head protein (5 copies)	* See gene VII
X	496-831	II(496-831)	DNA replication	* Separate gene X from gene II by inserting its sequence somewhere else in the genome. This will make it possible to modify X without modifying II.
XI (I*)	3916-4242	I(3916-4242), IV(4220-4242)	assembly

2. M13's closest evolutionary relative is the bacteriophage fd. Their genomes are about the same length, around 6400 bases, and their nucleotide sequences differ by only about 3.0%. Because their differences occur most frequently in some genes rather than others, it is less risky to re-engineer those genes that the differences occur on, since they are probably less critical to the virus.

3. "BBa_M1307 is not a standard biological part and does not belong in the registry."

• Response: Because BBa_M1307 is the entire genome of the M13K07 phage, it is more like a system than just a single part. According to the abstraction hierarchy, a "part" is a basic biological function that can be encoded as genetic material. BBa_M1307 is composed of numerous parts, such as the promoters, ribosome binding sites, and terminators for each gene. These parts come together to form devices that serve certain functions in the virus, such as proteins that enclose the system. Together, these devices sustain the virus and help it reproduce. However, the genome could be far more useful if its individual parts were broken down and biobricked, so that they could be studied individually or rearranged to create new systems.