Dspelke- Module 1: Genome Engineering

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M13 Genome

Protein Function Re-engineering Ideas
I Assembly Modifiy the gene so that the channels becomes less selective and thus allow other ions, molecules, and proteins to enter and exit the bacteria- see how this affects the life cycles of both the bacteria and the phage
II Replication of DNA + strand Alter the gene to make it more active and thus replicate DNA more frequently- see how increased DNA production affects phage growth
III Phage tail protein (5 copies) Modify the proteins that bind to the bacteria (and thus initiate the F pilus and infection) so that the bacteriophage canbind to and infect other types of bacteria- examine the varied life cycles that result
IV Assembly Alter the gene in such a way as to destabalize the outer membrane (e.g. no longer detergent-resistant)- test varying environments for phage survival rate
V Binds ssDNA Vary the activity of the gene and thus the competition between dsDNA formation and the sequestering of ssDNA- compare the results to find the optimum level of phage production possible
VI Phage tail protein (5 copies) Add some sort of tag to the gene that is only visible when p6 is outside of the bacteria- thus we would be able to determine when the phage has been secreted
VII Phage head protein (5 copies) Alter the gene so that p8 cannot be substituted for p5- see how this affects the phage (e.g. can it still be secreted?)
VIII Phage coat protein (2700 copies) Add a small protein to the gene that we would like to amplify becuase p8 is synthesized so many times- see if this method works and if yes, what applications could this be used for?
IX Phage head protein (5 copies) Modify the gene so that it can bind to bacterial surface proteins (like p3 does)- see if this allows the phage to interact with other bacteria (now that both ends can bind)
X DNA replication Altering this gene will also alter gene 2 so any alteration would affect both genes, so make any number of small modifications - see what interesting phenomena result
XI Assembly Modify the gene so that it is longer, hopefully resulting in a larger channel- see if this could allow multiple phages to pass through, thus making the channels more effective

M13.1 Refactoring

Dspelke- M13.1