Module 1: Genome Engineering, Day 1

Genome Re-engineering

Gene	# of Base Pairs	Function	Modifications
I	3196-4242	assembly
II	8268-831	replication of DNA + strand
III	1579-2853	phage tail protein
IV	4220-5500	assembly, forms channels in bacterial membrane
V	843-1106	binds ssDNA to make protein for packaging
VI	2856-3194	phage tail protein, supplementation to p3
VII	1108-1209	phage head protein
VIII	1304-1522	major phage coat protein, can adjust with size of genome
IX	1206-1304	phage head protein
X	496-831	DNA replication
XI	3916-4242	assembly, bacterial membrane, membrane channels

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.