How Gene Circuits Store Information

One of the great puzzles of cell biology is how information is stored, processed and passed from generation to generation at the biochemical level.

By far the most famous mechanism is the sequence of nucleotides in DNA. However, in recent years a number other data storage mechanisms have emerged, so-called epigenetic processes, and their role is under fierce debate. For example, the pattern of methyl groups attached to DNA seems to be an important data storage system as do modifications to the proteins that control how DNA is packaged.

Today, Georg Fritz at the University of Cologne and a few buddies put forward a new idea. They say that a simple network of genes can act as a conditional memory, that either stores or ignores information when it is told to do so. “The circuit behaves similarly to a “data latch” in an electronic circuit, i.e. it reads and stores an input signal only when conditioned to do so by a “read command,” say the group.

This memory circuit is essentially a modified version of the well known genetic toggle switch which consists of two mutually repressing genes and can exist in one of two states. The difference is that this circuit is controlled by the concentration of another protein. At high concentrations, the circuit is primed to store data in the form of another protein. At low concentrations, the circuit ignores what’s going on. That gives an extra layer of control over the simple toggle switch.

This a very simply design that has the potential to perform complex logic. Indeed, Fritz and co go on to show how such switches can combine to do just that. This is sequential logic which depends crucially on the history of input signals (as opposed to combinatorial logic which depends only on the present input signals).

That’s potentially very important. “Conditional memory would then enable cells to manipulate information “collected” under different conditions at different times,” say Fritz and co. In fact, exactly this kind of behaviour is observed in certain types of cell. We’ve looked at one example of apparently “intelligent” cellular behaviour that has exactly this property.

Fritz and co even go on to work out the properties that a conditional memory circuit should have. It should be able to respond to changes in the environment over a timescale of 30 minutes or so and yet be able to store information over many cell generations.

But here’s the rub: Fritz’s work is entirely theoretical and that raises an interesting and important question. Do conditional memory circuits actually exist in real genetic networks? Nobody knows.

They easily could and some fairly straightforward work should reveal their presence. If they don’t show up, that’ll be interesting too. It’ll mean that nature has found some crucial flaw in this circuit design or a better way of storing information.

Time get looking.

Ref: arxiv.org/abs/q-bio/0701011: Designing Sequential Transcription Logic: A Simple Genetic Circuit For Conditional Memory