Bacterial libraries for improving proteins
In a bacterial library, many different DNA sequences are introduced into the cells of a bacterial culture. Libraries are powerful tools for improving protein function.
What is a bacterial library?
A bacterial library is a large number of different DNA sequences (hundreds, millions or even billions), each of which is cloned into a vector and introduced into a bacterial cell, so there are a great many different DNA sequences represented within the individual bacteria in the library – one in each bacterium. It’s called a library because it contains so many different DNA sequences – just as a public library houses a great many books.
Read more about How to add foreign DNA to bacteria.
Bacterial library
In a bacterial library, each bacterium contains a different DNA sequence. Each DNA sequence is housed in the same cloning vector.
One gene, many versions
One important use for bacterial libraries is in improving the function of a protein or finding a protein with a new function. To make these libraries, scientists take as their starting point a gene that encodes a protein of interest. Every DNA sequence in the library is a slightly different version of that gene (a gene variant).
The bacterial cells in the library produce protein from the gene variants. Because the variants all differ slightly in their DNA sequence, there will be many slightly different versions of the protein too. Each will have a subtly different sequence of amino acids, and each is likely to function worse or better (usually worse!) than the original protein. In some cases, a variant protein may even have acquired a different function.
To use the library, scientists test the bacteria within it to see which of the many protein variants function best.
Read more about evolved enzymes.
A library for developing a cancer treatment
In David Ackerley’s lab (Victoria University), scientists are working to improve an enzyme that could form part of a cancer treatment. Their starting point is an enzyme that is somewhat effective at turning an inactive molecule into an active one that can kill cancer cells. Their aim is to create a version of the enzyme that can do the job much more efficiently.
In their search for an improved enzyme, David and his colleagues have made bacterial libraries that each contain many variants of the gene that encodes the original enzyme. They made their libraries by using a sloppy form of PCR (see below). Some of their most diverse libraries contain more than a billion unique versions of the gene.
See the animated video Directed evolution.
The article Catalysing chemical reactions with enzymes includes an animated video outlining in detail how enzymes work.
Improving enzymes to help fight cancer
In New Zealand, a new cancer treatment using enzymes made by directed evolution is being developed. The enzyme is targeted to cancer cells where it activates a prodrug. This multi-step process means the prodrug is only active in cancer cells and reduces side effects for patients.
Making gene variants
Scientists use several methods to make the gene variants that make up a library. One way is to use a version of polymerase chain reaction (PCR) called error-prone PCR (or sloppy PCR). In this technique, random changes to the gene’s DNA sequence are introduced each time the gene is copied. By the time the PCR is complete, billions of versions of the gene may have been produced.
Read What is PCR? to find out more.
Bigger is better
When making a library for improving a protein, scientists usually aim to clone as many different DNA sequences as possible. Why? Let’s say that only one in a thousand random changes in DNA sequence will improve the protein’s function (that’s a fairly typical estimate). The larger the number of unique DNA sequences, the more likely it is that one of the sequences will encode an improved protein.
Currently, the biggest libraries contain many billions of unique sequences. With numbers that big, it’s not hard to see why libraries are powerful tools for finding proteins with improved function.
