Just a quick word of warning up front. This is a very long entry. I spent some time thinking how to cut it down, but decided to post it in full length.

The cell, whether single bacterium, virus, or mammalian cell, is a fascinating and complex universe. Since the discovery of the cell hundreds of years ago, we have tried to understand how a tiny thing like that can function in so many wonderful ways and create so many colourful structures. Over the years, a mountain of research documents the discovery of individual cell compartments, then individual proteins and DNA, then complex mechanisms to express proteins from DNA, then individual signalling pathways, then posttranslational modifications of individual proteins, then even more posttranslational variations, then compartmentalised signalosomes, and so on and so on. The striking thing is that every time we dive deeper into the workings of the cell, we think we discovered the key to understanding what is necessary to make a cell work. But every time we get disappointed and we continue the search for even more detailed and previously undefined principles to make sense of what really goes on inside the trillions of cells of our bodies.

The original idea of cell signalling has been around for some time now and can be described as a sophisticated game of “Chinese whispers”. A stimulus, some kind of important message reaches the outside of the cell (receptor). There it knocks on the “door” of the cell and “whispers” any kind of information one can imagine. Things like: “can you please produce more of this or that, your neighbours really need it”, or “danger – we are under attack, produce a whole army of little soldiers so we can defend ourselves”, or “save energy – there is no food, so we all have to survive on the bare minimum”, or “you are old – thanks for all the hard work you have done, but now you have to kill yourself”, etc, etc. Then the guard on the door shouts out, “Hey! You! Protein messenger over there, come here!” Then the guard “whispers” the information to the messenger, the messenger takes off and tells the next, and then the next, and then the next, and so on and so on. Until the message reaches the head quarters of the cell, where the information is carefully evaluated and a response plan is formed. Then the scenario starts anew and whatever the response may be, travels in the opposite direction back to the outside.
Have you ever played “Chinese whispers”? How often does the last person repeat exactly what the first person has said? It never happened to me!

The mechanism of linear signalling, protein A tells protein B – protein B tells protein C – and so on, is of course a little bit more sophisticated and fool-proof then a game of “Chinese whispers” around a campfire, but nonetheless, the chance for errors must be huge! And now imagine that you are not on an empty football field, where one messenger can run freely to the next. Imagine you are in your local supermarket packed with the entire population of China and try and “Chinese whisper” to the guy at the other end of the store to send some milk over. What do you think he will send – if he sends anything at all!
The inside of a cell is cramped full with hundreds and thousands of proteins, lipids, RNA, and DNA. There is not much space to move around. This makes it even more difficult to imagine that single pieces of information are transported to and from different points within the cell. To get around this problem, the cell evolved a genius solution. Compartmentalisation! For example signals from a specific cell surface receptor are picked up by a number of signalling proteins and processed in specialised signalling complexes. This allows specificity of the signal, but also minimises the risk of disturbing or disrupting the signal.

But, compartmentalisation alone is not enough. Scientific research has revealed a seemingly never-ending number of posttranslational protein modifications that are used to convey information. Of course, in signalling complexes, information is passed on from one protein to another by direct interaction of the two. But further, each protein can be modified. The best known posttranslational protein modification is phosphorylation. Phosphorylation of serine, threonine, and tyrosine residues has been described of a long time and is a very important modification which plays crucial roles in protein interaction, protein conformation, protein activation and inhibition, and many more aspects of protein function. But other protein modifications have also been shown to be critically important, such as ubiquitination, sumoylation, acetylation, methylation, oxidation, nitrosylation, nitration, hydroxylation, and many more. Some of these modifications have strong effects and determine cellular locations of proteins or affect protein stability. But others seem to have very subtle effects, such as nitrosylation for example. Although there is some evidence that nitrosylation can affect protein activity, it is more likely that it is a modulator of protein activity, setting a threshold which determines the level of stimulus required to lead to signal propagation.

So it seems that there are several levels of organisation and regulation which control signal propagation. Like in our game of “Chinese whisper”, some people around our imaginary fireplace will hear a little better than others, some will be more or less influenced by the many beers they had, some might be thinking about the pretty girl sitting across from them, and others might be thinking about work or the stars. All this will influence and change the way they will hear that little piece of information they are supposed to pass on – unchanged!
In our cell, we will have protein interactions, protein compartmentalisation, and protein phosphorylation, which will have strong effects on signal propagation. But on top of that, there will be a layer of subtle modifications such as nitrosylation and oxidation which will fine-tune the information.

Imagine that a cell is hit by hundreds of signals and stimuli at the same time. Some of them will be activatory, others inhibitory, some will tell them to produce protein A and others will tell them to stop producing protein A. How can the cell decide what to do? The answer is a balance of activatory and inhibitory signals. Whichever comes out on top will be sent to the control centre. BUT, what if activatory signals win one minute (or second) and the next minute inhibitory signals are stronger? Will the activatory signal arrive at the control centre and tell them: “Hey, lets go, make protein A!”, and then the next moment the inhibitory signal arrives and shouts: “Stop, stop, don’t make that protein!” This sounds like a lot of wasted energy to me! And cells do their best not to waste any energy, because it is a lot of work to make enough energy to keep the whole thing running.
So, there must be a way for the cell to “remember” what kind of signals have just been sent in order to evaluate if it makes “sense” to send the next signal. But how is this done?
Of course, some of you will say, no signalling pathway is isolated and signals don’t travel uncontrolled from place A to place B. True, many signalling pathways converge several times and activatory and inhibitory signals cancel each other out or magnify each others message. But, nonetheless, a lot of energy is used to send a signal half-way, so why do that, if there is a good chance that it will be shut down half-way to the control centre.
The answer could be posttranslational modifications such as oxidation and nitrosylation. They both are the result of oxygen radicals or nitric oxide gas produced inside the cell. In contrast to phosphorylation and other strong posttranslational modifications which are very local and generally require direct protein-protein interactions, oxygen radicals and nitric oxide are free to diffuse throughout the cell, affecting many proteins from different signalling pathways at the same time. Because of this, they could act as a sort of “short-term-memory”. Let’s propose that our cell has just been exposed to a lot of activatory signalling, then the level of protein nitrosylation and protein oxidation could reflect that. As a result of that, additional activatory signals could be held back or slowed down, because the cell says: “Well, there are already signals on the way that say the same thing.”, however, if inhibitory signals arrive, the cell could hold them back and say: “Let’s just see what happens. If more of those arrive we will send them out, but for the moment, let’s just wait and see.” Imagine all the energy our cell could save by efficiently controlling which signals to send and which to hold back!

Of course this is an over-simplified image of what goes on inside each and every cell, but it also gives a good picture of the complications that our cell has to deal with. However, with the discovery of more and more posttranslational modifications and more and more tools the cell uses to control and fine-tune cell signalling pathways and networks, is it realistic to expect the science community to come up with a representative and accurate model of cell signalling networks? Of course, our understanding of signalling networks will become better and better in years to come, but what else will we have to add to the list of factors which influence intra-cellular signalling events? What if it is not only what goes on inside our cell that matters? What if our thoughts, our emotions, and other external factors play a role too? How will we realise that, and even more important, how will we measure and investigate that? Furthermore, will those efforts ever lead to the proclaimed goal? Will it be useful to know how these fine-tuning mechanisms work, i.e. could we make efficient drugs to manipulate cell signalling on such a sophisticated level? Would it be better to take a big step back and look at the big picture and try to assess these processes using a holistic approach, rather then digging deeper and deeper until there is no point of return?