Over the years I have started several cell simulations, some of which have even 'lived', but by far the most complete and complex simulation, was of heterocysts (and their evolution). The main reason for its completion was that I managed to curb my natural tendency to cram in ever more details. I hope to write about that simulation and its results at some point, and maybe even add the Java program, but first I want to explain what heterocysts are and why I think they are an interesting subject to simulate. You could of course read the Wikipedia page about heterocysts, which is actually one of the few pages on Wikipedia that I created. But I will try to write a better description of heterocysts here.
Nearly all organic molecules are made from only a few types of atom: carbon, nitrogen, hydrogen and oxygen. These atoms are abundant in our environment, however not all the atoms are available for organisms to metabolise. For example, diamond is pure carbon, but I don’t think there is a single organism that can metabolise diamond and use the carbon to built its own molecules. Similarly, carbon dioxide is freely available in the atmosphere (albeit at only 0.038%), but we animals are unable to utilise it. Fortunately for us, plants (and other organisms, such as algae and some bacteria), can photosynthesise; they use energy from light to rip carbon atoms out of carbon dioxide (releasing oxygen) and use them to build sugars, fats and proteins, which we can metabolise.
Hydrogen and oxygen are readily available to all organisms in the form of water, which just leaves nitrogen. Nitrogen gas makes up 70% of the atmosphere, so is readily abundant. However, the nitrogen atoms in nitrogen gas are joined by a triple bond, which makes the molecule very inert. In fact, one source of fixed nitrogen is through lightning strikes, which are one of the few phenomena powerful enough to tear the atoms apart. Fortunately, some organisms have evolved an enzyme called nitrogenase, which converts nitrogen gas into ammonia, which they and other organisms can metabolism.
Nitrogenase uses a lot of energy, hydrolysing 16 molecules of ATP (the cell’s short-term energy store) for every molecule of nitrogen gas fixed. Nitrogenase is necessarily a very reactive enzyme: it has to break the triple bond in molecular nitrogen. This requires a transition metal complex (which contains molybdenum, vanadium or iron) and so is highly susceptible to damage by oxygen. As a result, most organisms that make nitrogenase live in anaerobic conditions, such as deep under the soil.
Combining Photosynthesis with Nitrogenase
Since all organisms require fixed carbon and fixed nitrogen, for a organism to be self-sufficient, it must combine photosynthesis with nitrogenase. This poses organisms with a challenge, since photosynthesis produces oxygen, which nitrogenase is so sensitive to. As such few organisms can fix both carbon and nitrogen.
One group of organisms that appear to achieve this feat of fixing nitrogen and carbon are the legumes, such as pea and soyabean plants. These plants photosynthesise like all plants, but also produce fixed nitrogen, which is why they were traditionally used in crop rotation – they increase the amount of fixed nitrogen in the soil, thus reduce the need for nitrogen-containing fertilizers. However, legumes do not actually fix nitrogen themselves; they allow themselves to become infected by nitrogen-fixing bacteria called rhizobia, forming a symbiotic relationship with them. Rhizobia form cysts or nodules in the roots of legumes, metabolising fixed carbon (i.e. sugars) produced by the plant. In return, rhizobia use nitrogenase to fix nitrogen gas, providing themselves and the plant with fixed nitrogen. The root nodules have a low oxygen concentration, partly due to a protein called leghaemoglobin, which is produced by the plant. Like haemoglobin in our blood, leghaemoglobin binds oxygen (only more strongly), thus helping to protect the nitrogenase enzyme.
Some cyanobacteria (such as Anabaena sperica and Nostoc punctiforme), however, have accomplished the seemingly impossible task of fixing both carbon and nitrogen. Like legumes, these bacteria solve the problem by separating the tasks of carbon fixation and nitrogen fixation into separate compartments. Rather than have different organisms carry out the two reactions, individual cells specialise to carry out either photosynthesis or nitrogen-fixation and then exchange the products (a bit like two people or economies specialising in two different type of production then trading). The cells specialised in nitrogen-fixation are called heterocysts, due to the fact that they are different from the normal, vegetative (photosynthetic) cells and they have a cyst-like appearance.
In becoming a heterocyst, cells must synthesise the enzyme nitrogenase, but they must also halt photosynthesis. They achieve this by degrading the group of enzymes that make up photosystem II, which is the part of the photosynthetic machinery that produces oxygen. Heterocysts also produce additional cell walls, which help to protect them from oxygen (which is still produce by neighbouring cells). They also produce proteins that bind oxygen like leghaemoglobin in legumes. In order to cope with the increased energy demand of nitrogen-fixation, heterocysts also increase their rate of glycolysis – an set of reactions that produce energy from glucose. Since heterocysts are unable to produce glucose by photosynthesis, it is drawn in from neighbouring cells through pores. Fixed nitrogen flows through these pores in the opposite direction, from the heterocysts to the vegetative cells.
Specialisation (or differentiation) of cells is common (maybe ubiquitous) in multicellular organisms. For example, humans have cells that are specialised for roles in the heart, lung, liver etc.. However, it is very unusual for single-celled organisms, such as bacteria to differentiation. In fact, a filament of cyanobacteria containing heterocysts could be viewed as a single multicellular organism with two tissue types. In further support of this idea is the fact that the formation of heterocysts is a terminal differentiation – that is, not only is a heterocyst unable to revert back to being a vegetative cell, it is also unable to divide. This makes a heterocyst like the majority of the cells in an animal’s body – only stem cells are able to divide and replace cells such a nerves or red blood cells, and only the germ cells (sperm and eggs) can go on to produce a new organism. Some heterocyst-forming bacteria also differentiate to form spore-like cells called akinetes or motile cells called hormogonia.
For all collections of cells that specialise (such as multicellular organisms), it is vital that the right number of cells specialise in each task and that the cells specialised for each task are in the right position. For example, in humans, we don’t want all of our cells to become lung tissue, and nor do we want our cells in our brain to become liver cells. How multicellular organisms develop is a very complex question. Heterocysts provide a simple model that can help us to understand the principles of development since filaments of heterocysts-forming bacteria have only two cell types, and the pattern of cells is one-dimensional.
When fixed nitrogen becomes limited, it is important that the right number of cells become heterocysts: too few and the filament of cells will still be limited by fixed nitrogen, too many and fixed carbon will become limited as fewer cells photosynthesise and more sugar is metabolised to power nitrogenase. It is also important that the right cells in the filament become heterocysts: it is optimum to have the heterocysts evenly spaced along the filament, so fixed nitrogen is more evenly spread along the filament. If two heterocyst are next to one another on the filament then they will compete with each other for fixed carbon. In nature, heterocysts normally form about once every 9 to 19 cells.
How can a filament of cells create the right pattern when there is no central control? Each cell acts autonomously and can only directly communicate with the cells on either side of itself, yet each must decide whether or not to become a heterocyst. To make the problem more complex, the vegetative cells are constantly dividing, so even once the pattern is established, heterocysts will move further away from one another. Once heterocysts are about 19 cells apart, the cell halfway between them must somehow ‘know’ it is in the middle and become a heterocyst, thus reducing the distance between heterocyst to nine cells. [I should probably draw a diagram to illustrate this.]
I’ll write in a later post (or three) about how this is done, how I modelled heterocysts and this problem, and an analysis of what happened when I allowed my model to evolve a solution to the problem.