Thomas Pollom: Module 1 Day 1

1. The major writing assignment for this module will be a description of your M13 renovation work. Use the summary in your lab notebook to start a table on your wiki user page to organize your thoughts about the existing genome. Generate a table that lists each gene and any re-engineering ideas you have for it.

Gene	Location	Overlap	Function	Re-engineering Ideas
I	3196-4242	Gene XI from 3916 to 4242, and gene IV from 4220 to 4242	Forms channels for phage secretion	Change protein such that it denatures at a particular temperature or pH so that secretion of phage from bacteria can be regulated
II	8268-831	Gene X from 496 to 831	Initiates Replication	Add some steric hindrance to the active site of the protein in order to slow down the rate of replication
III	1579-2853		Forms rounded tip. Allows phage to enter bacteria	Change length or structure of protein in order to alter the rate of phage infection
IV	4220-5500	Gene I and XI from 4220 to 4242	Forms channels for phage secretion	Change protein such that it denatures at a particular temperature or pH so that secretion of phage from bacteria can be regulated
V	843-1106		Binds to single stranded phage genome within bacteria cells	Add a weak self binding motif to the protein so that each secreted phage might have multiple genomes in order to see the effect on the phage's behavior
VI	2856-3194		Forms roudned tip. Allows phage to enter bacteria	Change length or structure of protein in order to alter the rate of phage infection
VII	1108-1209	Stop codon overlaps with Gene IX start	Forms blunt end of phage	Add a protein III binding motif in order to produce long phage chains
VIII	1301-1522	Start codon overlaps with gene IX stop	Major coat protein	Make metal oxide binding motifs in order to create virus templated nanowires
IX	1206-1304	Start codon overlaps with Gene VII stop, and stop codon overlaps with Gene VIII start	Forms blunt end of phage	Add a protein III binding motif in order to produce long phage chains
X		End of gene II from 496 to 831	Assists DNA replication	Change start codon to another codon which does not significantly affect the effectiveness of pII and then copy gene X elsewhere in the genome so that I can alter the two genes independently
XI	3916-4242	End of gene I from 3916 to 4242, and gene IV from 4220 to 4242	Forms channels for phage secretion	Change protein such that it denatures at a particular temperature or pH so that secretion of phage from bacteria can be regulated

2. 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?
According to Robert Webster of the Duke University Medical Center, f1 and fd phage are most similar to M13 phage. All three are in the Ff class of the filamentous phages. The DNA sequences of these three phages shows them to be 98% homologous.

3. 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."
According to the registry, "The M13K07 sequence includes the entire M13 genome as well as a sequence from pACYC177 bearing the p15a bacterial origin of replication and a kanamycin resistance gene." We discussed in class that a "part" is a basic biological function that can be encoded as genetic information. Thus, I agree that BBa_M1307 is not a standard biological part because it encodes multiple biological functions. It would be better classified as a biological device, or probably even more appropriately as a biological system.