Team:ETH Zurich/Project/Overview

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== The Minimal Genome Project ==
== The Minimal Genome Project ==
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Overview
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The reduction of a genome to its most fundamental parts is a task of broad biological interest which has already long been sought for. It addresses the question of which set of genes are absolutely necessary to support life in its most primitive form.
The reduction of a genome to its most fundamental parts is a task of broad biological interest which has already long been sought for. It addresses the question of which set of genes are absolutely necessary to support life in its most primitive form.
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Several approaches have been taken by a number of scientists to tackle this problem. Recently, a cleaned-up version of ''E. coli'' containing a 15% smaller genome has been presented by Posfai et al. In this approach, however, targeted deletion of genes was applied. Therefore, a strong bias towards which genes could be dispensable was inevitable.   
Several approaches have been taken by a number of scientists to tackle this problem. Recently, a cleaned-up version of ''E. coli'' containing a 15% smaller genome has been presented by Posfai et al. In this approach, however, targeted deletion of genes was applied. Therefore, a strong bias towards which genes could be dispensable was inevitable.   
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Our approach of creating an ''E. coli'' showing a minimal genome is largely free of any bias. This is achieved by short pulses of ''in vivo'' expression of a restriction enzyme and a ligase. The restriction enzyme randomly cuts the genomic DNA. If two cuts or more are generated within one pulse, a chromosomal fragment might be excluded before the ligase performs its job of religation. This results in the random deletion of chromosomal fragments.  
Our approach of creating an ''E. coli'' showing a minimal genome is largely free of any bias. This is achieved by short pulses of ''in vivo'' expression of a restriction enzyme and a ligase. The restriction enzyme randomly cuts the genomic DNA. If two cuts or more are generated within one pulse, a chromosomal fragment might be excluded before the ligase performs its job of religation. This results in the random deletion of chromosomal fragments.  
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Though the chance of this event to happen is rather low considering a single cell, it becomes likely when looking at an entire population. However, this creates the need of having to select for cells which have successfully eliminated parts of their genome. Since manual selection is obviously impossible considering the tremendous number of cells in a culture, it would be convenient to equip cells carrying a small genome with some kind of growth advantage enabling them to outgrow the rest of the population in a continuous culture.  
Though the chance of this event to happen is rather low considering a single cell, it becomes likely when looking at an entire population. However, this creates the need of having to select for cells which have successfully eliminated parts of their genome. Since manual selection is obviously impossible considering the tremendous number of cells in a culture, it would be convenient to equip cells carrying a small genome with some kind of growth advantage enabling them to outgrow the rest of the population in a continuous culture.  
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Therefore, we opted for putting a constraint on nucleotide synthesis to make DNA replication the rate-limiting step of proliferation. In this case, cells with a smaller genome should replicate and therewith divide faster than cells carrying larger genomes.
Therefore, we opted for putting a constraint on nucleotide synthesis to make DNA replication the rate-limiting step of proliferation. In this case, cells with a smaller genome should replicate and therewith divide faster than cells carrying larger genomes.
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Finally, after the last pulse has been applied, the ''E. coli'' carrying our minimal genome will take the lead in our culture.
Finally, after the last pulse has been applied, the ''E. coli'' carrying our minimal genome will take the lead in our culture.
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Revision as of 16:23, 26 October 2008


The Minimal Genome Project

Overview


The reduction of a genome to its most fundamental parts is a task of broad biological interest which has already long been sought for. It addresses the question of which set of genes are absolutely necessary to support life in its most primitive form.


Several approaches have been taken by a number of scientists to tackle this problem. Recently, a cleaned-up version of E. coli containing a 15% smaller genome has been presented by Posfai et al. In this approach, however, targeted deletion of genes was applied. Therefore, a strong bias towards which genes could be dispensable was inevitable.


Our approach of creating an E. coli showing a minimal genome is largely free of any bias. This is achieved by short pulses of in vivo expression of a restriction enzyme and a ligase. The restriction enzyme randomly cuts the genomic DNA. If two cuts or more are generated within one pulse, a chromosomal fragment might be excluded before the ligase performs its job of religation. This results in the random deletion of chromosomal fragments.


Though the chance of this event to happen is rather low considering a single cell, it becomes likely when looking at an entire population. However, this creates the need of having to select for cells which have successfully eliminated parts of their genome. Since manual selection is obviously impossible considering the tremendous number of cells in a culture, it would be convenient to equip cells carrying a small genome with some kind of growth advantage enabling them to outgrow the rest of the population in a continuous culture.


Therefore, we opted for putting a constraint on nucleotide synthesis to make DNA replication the rate-limiting step of proliferation. In this case, cells with a smaller genome should replicate and therewith divide faster than cells carrying larger genomes.


Finally, after the last pulse has been applied, the E. coli carrying our minimal genome will take the lead in our culture.

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