Assignment: Make a set of rules for redesigning a bacterial genome based on biological knowledge and transposon bombardment data. I have provided an Excel file that lists all the genes in Mycoplasma mycoides JCVI syn1.0, and tells you what transposon bombardment revealed about each gene. By that I mean whether it is essential (e), not-essential (n), or whether a disruption of that gene causes impaired growth (i). If one were to design an algorithm capable of designing a minimized cell capable of rapid growth, what are the rules one would use to program the algorithm.
Useful file for homework here:
EMycoplasma mycoides JCVI syn1.0 transposon bombardment results
Group Homework PDF
Our Minimal "Living" Cell Algorithm:
1. Find common essential genes between already “minimized genomes” and target bacterium
2. Assemble a genome for target bacterium (GC content,
mutations) and transplant it.
3. See if the bacterium can grow fast enough. If not, decrease sensitivity of first step matching.
Extra: Compare essential genes with synthetic minimal cell genes and find what it is extra.
From the diagram below found here @ Essence of life: essential genes of minimal genomes
we propose to use the first method (a)
