Thomas Pollom: Module 1 Day 1

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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.

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