Module 1: Genome Engineering, D1

HaoSuperM13: Genome Re-engineering

Gene	Location in Genome	Function	Overlap/Modification Advantage/Disadvantage	Re-engineering Ideas
gI	3196-4242	Assembly, Channels for Exit	g11 is inside g1, g4 starts at the end of g1's sequence |A: Since g1 and g11 have same function, if I wanted to affect assembly overall, I would modify g11 and affect g1 D: If I only want to change g11, I would change g1 anyway	I would want to change some function that would modify the channel for exit, perhaps making the channel larger or smaller and seeing what is affected
gII	8268-831	Replication of DNA	g10 is inside of g2 |A: Since g2and g10 have same function, if I wanted to affect DNA Rep, I would modify g10 and affect g2 D: If I only want to change g10, I would change g2 anyway	I would probably stay away from this but if I wanted to add a GFP protein, I could watch both proteins or label g2 and g10 different fluorescence colors and see how they differ
gIII	1579-2853	Phage end, exits first	g3 does not overlap anything	Modifying this gene may render the phage useless as it may prevent the phage from exiting the hose cell. However, if it can be re-engineered to bind to proteins other than TolA, it may be a useful device for marking certain types of cells
IV	4220-5500	Assembly, forms channels in bacterial membrane	Same as gene I, perhaps deletion of one of these genes may provide information on how far the production of membrane channels may proceed
V	843-1106	Binds ssDNA to make protein for packaging	Would not change this gene too much unless want to examine effects on ssDNA versus dsDNA
VI	2856-3194	Phage tail protein, supplementation to p3	Altering this gene may have similar effects to altering gene III, which would allow for the examining of function/duty of p3 in infecting/exiting the hose cell
VII	1108-1209	Phage head protein	Fusing this gene with GFP may provide a targeting/marking protein helpful in observing phage/bacterial activity
VIII	1304-1522	Major phage coat protein, can adjust with size of genome	Altering protein affinity or allowing expression of certain proteins can allow the major coat protein to bind to objects, perhaps for marking or just for production of certain proteins
IX	1206-1304	Phage head protein	Same as gene VII
X	496-831	DNA replication	Similar to gene II, perhaps possible to control affinity for ssDNA or dsDNA so that more of one or the other may appear in a bacterial cell, this could be good or bad depending on whether we want more of the phage to be created and secreted or less
XI	3916-4242	Assembly, bacterial membrane, membrane channels	Same as gene I, IV

M13's Family

M13’s closest evolutionary relatives are the bacteriophages Fd and F1, both of which are filamentous phages. They all have single stranded DNA (ssDNA), and their coat proteins may have slight differences, causing the phages to vary in surface charges. The differences in nucleotides only diverge within a 3% margin, though their restrictions sites are in different sequential placements, because they all originate from the bacteriophage family Inoviridae.

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

BBa_M1307 is the M13 genome with the additions of an origin of replication of the pACYC177 bacterial DNA sequence and the kanamycin resistance gene. According to the levels of abstraction defined in class, a ‘part’ can be only be a sequence of DNA that encodes for a biological function that may be utilized by a ‘device’ or ‘system’ to perform a specific task. Not only can BBa_M1307 perform many functions such as the ability to infect a host cell, replicate its genome, assemble proteins, resist kanamycin and exit a host cell without causing lysis, it itself is made up of several parts, and thus acts more like a ‘device’. If BBa_M1307 can be broken down and re-engineered into a new ‘device’, used for further analysis or just simply for parts, the modification may make it more acceptably classifiable as a ‘part’ rather than something farther up the abstraction ladder.