Saturday, 1 March 2014

Understanding genomes through bacterial viruses: the Lambda Project for Y10. Part I

E.coli under attack from
phage lambda
The viruses that infect bacteria (or prokaryotes) are called bacteriophage (a combination of the Greek words bakteria, a staff or cane, in view of the common rod-like appearance of many bacteria under the microscope, and phagein, which means to devour). They are the most abundant organisms (see below) on our planet and are often simply called phage, for short. As with all viruses, they cannot replicate without "help" from the host they infect. You will be more familiar with the influenza (or flu) or the cold viruses, which are viruses that infect us. However, we stop short of referring to viruses and phage as true life forms, since they require help from the host cells that they infect. The image left shows the phage lambda being infected. Sometimes the phage burst open the cells with the release of thousands of phage particles (we call this the lytic phase). Alternatively the phage infect and then adopt a dormant phase, where they just sit and wait before some external event triggers the lytic phase. Bacteria carrying such phage are called lysogens. The switch between these two phases is controlled by a genetic circuit. This is a simple model for the decision processes that take place in us, although the system is much simpler. We are going to use a set of "molecular scissors" to investigate the genes that make up phage lambda.

Because viruses and phage require host cells to replicate (copy themselves), they are usually simple particles, with their genes (in the form of DNA or RNA) packaged in a shell, often made up of a small number of proteins. In the case of phage lambda (left), around 30-40 genes encode the same number of proteins requiring a total of just under 50 000 base pairs of DNA. The phage head and tail (right) are encoded by the phage. When the phage infects and "sleeps" it enters the genome of the host. When it is awakened, it leaves the host genome and sometimes takes some of the host genetic material with it. This phenomenon is known to occur in animal viruses too and was critical in the isolation of cancer genes, where certain cancers are transmitted by viruses.

Phage lambda is encoded by just under 50 000 base pairs of DNA in a linear chromosome. Last week you used an enzyme called EcoRI to cut the DNA into pieces and then used agarose gel electrophoresis to "visualise" this. Last week's experiment was aimed at ensuring you could carry out the manipulations (microlitre volumes etc) sufficiently accurately for us to carry out the detailed mapping that you can see left. I have posted your data on the Innovation Lab Portal. We have some work to do to get the gels up to scratch, but we will have last week's experience behind us. I shall explain the use of these "molecular scissors", or restriction enzymes in Part II. They will help us map the genes on the phage, with the help of the lambda genome sequence that we can easily access through NCBI.

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