Category Archives: Science

Prions, just what the….? 

It has been a good decade since I worked  in biotech and back then there was still a great deal of concern about BSE and CJD as fatal diseases with serious epidemiological consequences and many unanswered questions as to the mode of infection and replication. 

Thirteen years on from BSE gels at Invitrogen being the big thing, Prions remain a bit of a mystery and pose questions about the very origin of life as we know it- invasive, replicating and diversifying!

What Do We Seem to Know About Prions? 

Prions are very odd, they are an enigma to molecular biologists and may prove to be a factor in more disease aetology than we currently know through the more severe and easy to diagnose brain and CNS diseases we know today. In theory a single abbertant protein can precipitate many other proteins in a kind of chain reaction where they then semi crystalise in a new, stable state. This can be described as abberrant and altered protein folding, rather like a slinky *TM spring you are playing with which suddenly gets a little damaged and forms a new shape. 

. As the cell perhaps make more proteins to replace those which lose function, then the chain reaction continues until enough of the cell machinery is either overloaded or the cell is full of prion material and is subject to cell death and lysis. Thus prions are released to infect, or you could say damage other cells, in what many argue is a purely chemical way.

Protein folding is something which happens usually within cells as the peptides are being built on or through the Ribosomes, a nano 3D printer nature happened to fall upon over a billion years ago, or they are meddled with by other entities in the cell,  including  ions and importantly for Prion mechanistics, other proteins with which they form useful big proteins with, like haemoglobin or enzymes. Where as on sister or cousin protein will guide a newly made ‘wobbly’ string of amino acids, a peptide, into being a useful part of the cellular machinery, a Prion will cosey on up to it, and make it fold differently, into long beta sheet folds, which become like fibres in the cell once they start to precipitate. It is theorised that a prions could cause pre-made proteins to fall into a new state, by sliding on up beside them and coaxing them into spreading out and lieing beside them.A chain reaction may then ensue from protein to protein, within fairly specific classes of proteins, which for some reason are usually found in central nervous tissue so far at least,.. These ‘prionised’ proteins become far more stable than other forms, and difficult to get rid of, blocking up the cell and leading to misfunction and eventually cell death.

Ye Cannae Defy the Laws of Physics Jim….

 There is a fundamental bit of philosophy and physics here, that molecules will find a most stable state and persist.  Biological enxymes are inn contrast rather dynamic molecules, where often parts of the molecule act like hinges, or even become temporarily covalently bound to the ‘ligand’ which they are acting upon. Some complex proteins like Haemoglobin, harness both other organic molecules (porphyrins) and metals, iron of course in the case of most higher organisms. These complex proteins then are often not verry stable in terms of structure   or become a little ‘poisoned’ as catalysts. Hence our excrement is brown, as the unstable haemoglobin protein aggregates burn out so-to-speak,  and the more toxic break down product from their catabolism, bilirubin, gets secreted in our guts. 

Plaques they are called then  these aggregates of duff, structurally stabilised  protein, or fibrils to be more precise to mol’biologists. An analogy would be a seed crystal in a salty solution which creates a large, branching crysal, or for example a spec of dust which allows super cooled water in clouds to crystalise and become snow flakes. There is a natural, entropic tendency to assume certain structures and a single, small entity precipitaes out the bigger structure, which may be non homologous or semi homologous in the case of the proteins in animal cells. Without that seeding entity, there is no crystalisation. 

Molecular Intelligence or Pure Chance Entropic Effect ?

One of the main lines of thought is that Prions are a purely chance phenomenom which has arisen through a classic of evolution: perpetuation by surviving, accumulating and replicating. In that though there is a fundamental dileman or even oxymoron. Do Prions really replicate via a protein to protein route or is there as many suspect a viral type of nucleic acid vector? 

In theory though we could be looking at something which occurs by pure chance and is related to some fundamentals of the thermodynamics and entropy of protein folding. It could be that there is a weird chain reaction which is purely physical in nature, and propagates purely by re-release of ‘prionised’ proteins into the infected creature and then out into other  creatures. This is no bad stance to take on the theory, because it is known that CJD is spread from cattle to humans via consumption or exposure to body fluids and materials at work. 

However that stance is equally as enticing for an infectiious agent which uses a nucleic acid. Or as was propsed by some headline grabbers at the time, that there was a new route to replication of proteins outside the central dogma of DNA-RNA-Peptides. That a single protein agent could instruct the cell’s DNA , or mRNA to do something odd and cause proteins to build up and kill the cell, thus perpetuating the ‘species’.

. At one point it was believed that the Prion acted like a virus, devoid of nucleic acid code, but with a kind of proxy message – it could perhaps turn on genes which favoured certain protein production which then lead to more prionisation and inevitably, some proteolysis would create new prions. Or even more sinister, that the seediing Prion could both kill the cell having made more of itself by directly controlling the nucleic acid pathways. This would point to a most uncomfortable ideom for geneticists, the instructive method of gene control, where proteins tell the cell how to change, and the cell line alters, rather than the mechanism of natural selection being at work. There are though some special cases where this happens, in immunogenetics at least as far as I know, perhaps elsewhere, but that is for very specific purposes. Is there then a dastardly signal and almost alien life form mechanism behind Prion replication? 

No Signs of Message So Far?

More than a decade on from the BSE -CJD – Scrapie Pie scare in the UK and around the world, researchers have not found any nucleic acid or other set of instructions encoded in protein or anything else which would point to a little mastermind of an infectios agent behind the Prions. It could be though on the one hand that they just havent been looking in the right places or something has been taken for granted. 

On the other hand it could just be that we have that grain of sand in the mother of pearl, which makes a pearl in the one cell that is, which then bursts down to a million new grains of sand and is infective and replicative that way. Furthermore, if this latter be the case, it could be purely the fortuity of probability,  that these fibril bodies are proteolysed by cellular immune systems or post cell death, and a very few become ‘ seed prions’ as a matter of due course, given enough of them. .

Prions Are Perhaps a Clue to the Origins of Life 

We get back into the concept of the very origins of life, especially when the space ship Cassini finds liquid water and organic compounds on a moon of Saturn, and Mars , well is NASA holding back on us a bit here?  

Prions exist and propagate because they can exist and propagate. This is very much the kind of concept of very early life, when it has been hypothetised that peptides predated nucleic acids as the means of firstly ‘precipitating’ enough material so as to be able to replicate, and then to do this replication accurately enough to spread the proto organism. Proteins (peptides) very often naturally ligate metal ions, which then create a lot of useful and immensely powerful chemistry – the power to split water, carbon dioxide, oxygen dimolecules and nitrogen, phosphorous and sulphur compounds. to other thermodynamically useful ends. More replication, more accumulation of building blocks, more interesting things being built, chance  events. 

The ‘primeval soup’ then gets lumpier and lumpier as a string of chance events favoured by thermodynamics snow ball into ‘species’ of proto-organisms, which then either compete with each other, perhaps eating each other, or cooperate with each other. It is theorised now due to the deep hot volcanic vents of the ocean floor, that life could have evolved in many places on earth to the single celled forms. The idea of the miracle, the genesis event only once in the universe, is really put up against the possibility that carbon /nitrogen/phosophorous life is an inevitability if you have the right chemical buiolding blocks and environment. 

Prions – Does Nothing Direct Them, Other Than Thermodynamic Fate?

Personally I am kind of on the fence, just in case because they may well find an infective agent when and where they least expected  it. If Prion ‘seed’ proteins are only needed in small qauntities for the disease to progress, and there is then an advantage to the dark knight infective agent behind the scenes to use this, then it may be that the little nasty thing is a real lurker, or in fact nothing described by science so far – a protein only virus perhaps? On the other side of the fence, there is the pure entropic beauty of a self propagating protein system, which has no forward looking ambition, there is no design in its madness, it purely is a phenomenom because it can be one due to the laws of physics and chemistry. 

Here then we get back to the origins of life and how a ‘soup’ of what ever nutrients and metal ions, could kind of simmer for a while and start to do interesting, large molecule based chemistry which replicated itself. If you replicate something by chance, you get more of it, it accumulates, it propagates. In a more complex way, but yes you can say like a nuclear chain reaction in a fission neutron reactor. Over time we see that which persists, that which thrives, that which adapts. Most of all we see the mechanisms of the universe and life are fundamental and undeniable.

Perhaps indeed Prions are either a very old hang over from the earliest forms of life, which nature never quite managed to kill off. Or perhaps prions are an example of  co-evolution, a secondary meta-genesis event fortuitated by some vagiaries of proteins in brain tissues in particular.  These particular protein systems which were not present in earlier evolution when DNA based systems were kind a pressure to select against Prion type activity as being dangerous and competitive to the new, robust and ‘blindly intelligent’DNA driven core of life to come. Hence perhaps prions can do their dirty work and spread purely because they damn well can, it is an inevitability given the right set of factors.. 

Questions Around Allelic Exclusion, 30 Years On

It’s 28 years since I studied allelic exclusion in B lymphocytes as my paper based undergrad’ thesis. I kind of fell upon the concept, as it always bothered me from the first days of understanding simple Mendelian genetics – how does it all work with two copies of a gene yet only one phenotype?

Well Mendel of course, cheated. He actually ignored strains of peas whose flowers bred through to pink, instead of those which bred pure white or red. Genetics is always throwing up complexity around some central simplicities, and as with the Human Genome Project, scientists go off on keep-it-stupid-simple at their hazard.

In allelic exclusion in certain types of  white blood cells, there is some very interesting genetic engineering, and sorry dear creationist, you can see evolution happening in your own bodies if you care to study the molecular mechanisms. At some point a white blood cell decides                                                                                                                                                                                                                                   to make one very specific antibody which has the purpose of             very specifically locking onto a potential  disease causing agent. This is then locked and in effect it becomes a memory cell if you like, which can then explode in a clonal type way to produce thousands of these cells all of which are identical to fight a disease currently threatening the body, or doing so in future. Earlier on in the story, the cells have undergone some degree of evolution, firstly by being selected as fairly good matches for that ‘pathogen’ or antigen to be more accurate, and then having to select which one of two versions of the gene for the antibody will be the one which is most suited to the job at hand after in fact the cell induces some very specific mutations, or internatl genetic engineering, to alter small parts of the antibody such that it may become more specific and thereby the antibodies will bind better and discriminate between this specific threat and others in a manner much enhanced over the earlier incarnation of the cell line.

So one gene gets switched roundly off, while the other copy, which is a little different due to this ‘hyper mutation’ is kept for the life of the new cell line. If i remember correctly, there was only one iteration of this process, but of course it occurs over a population of white B lymphocytes and other related antibody producing cells, so that a diversity is then honed down into a more targeted set of cells which can tackle disease better. So we see natural selection at work, every day , in our own bodies with mechanisms of molecular directed evolution to boot!

Now this was thought to be a very specific mechanism, the exclusion of one of the two copies from further use in the cell. However back to Mendel. It seems to be very wasteful to have one copy of the gene which is recessive, or presumably non functional? White flowers it seems are default no colour when two copies of the white, failed gene are present. It just seems a waste of space.

Well in fact recent research amongst relatively inbred populations including Iceland and an area in Pakistan, show that in fact humans in such small gene pools harbour upto 7% inactive gene copies. It may seem that prevalence then of genetic diseases would be much higher, but althouugh some typical genetic linked diseases like Huntingdons are present, there is actually not a correspondingly higher rate of disease in accordance with the inbreeding and this high percentage of ‘knocked out’ genes.

Here we see again that a simple route can reveal complexities and the golden rules can and are broken, wihtout perhaps the exeptions quite proving the rule. We find that a gene in the genome, on the chromosome, can be swithced on and off intermittantly, or more locked away and this can vary between copies, sometimes the paternal is less likely to be switched on than the maternal copy. The simply methylation of chromosomal DNA can affect this. Also the gene product need not be a protein, but can be an intermediary control element. And if there is a final protien as in the good old central dogma of genetics, then it can vary in how it is constructed from the one gene, or be made up of several genes spliced together at the messenger RNA level. 

Oh dear, Genetics is big and scary and the Human Genome Project to some extent, only confused us more. There were fewer genes than expected, and a now it seems there may be more inactive, fautly genes that first thought. Also there may be redundancy of alleles, or multiple alleles of the same gene, or perhaps gene products can be cobbled together to make up for a K/O’ed gene at the mRNA level. It suddenly became important to study diversity between individual genomes so as to try and understand what was going on. 

From my point of view then I always said that in Genetics and molecular biology, there is simplicity to be found in diversity, and that the abnormal informs the normal. There is a fundamental truth that in studying one fairly obscure genetic phenomenon, we find a universal truth, yet we cannot understand a universal trith fully without considering diversity.

Big science has kind of speeded things up, but also quite possibly used up huge resources in uncovering issues which were already there as in the last paragraph . We need to look at the detail but also how varied each detail is. So if you follow one obscure detail, like allelic exclusion in B cells, then you find out a lot about it, in fact so much that in this case specifically, it seems it is just an obscure mechanism . for time being. If you give yourself a bigger job, then yes you get more done in terms of this diveristy, but you are building a bigger stick to beat yourself with as that diversity then starts to obscure the universality in mechanisms. However Big Science came with a lot of public and private funding so we cannot complain from that point of view, and a lot of processes which were tedious and manual when I was working in labs (with the first commercially available multi well PCR thermal cycler with digital control) have been either fully- or semi/automated and results are as likely to be read on a computer screen than in a ‘petri dish’so to speak.

The older, more patient and pedantic me would suit being a scientist today because I am quite computer literate and like solving puzzles,. At the same time being locked into using standard equipment means that you perhaps loose some pioneer spirit and perhaps come up with less new technique innovation, which is also very enabling in terms of being able to do new things, if not do the same thing thousands of times over accurately and automated. 

We come back to the whole simple argument which is really about sex. Why have diploid organisms which breed sexually? Well in fact those industrious and ingenious little B cells have the answer. We need diversity to survive and evolve. Without diversity there would be no real selective evolution, one species would tend to get whiped out, as we saw with for example the potatoe blight of the 1800s which was from all plants stemming from a tiny number  brought back from S. America. We need sexual reproduction and sexes because it means we can recombine good survival packages of genes to then meet the challenges of the environment. Sex speeds up evolution by this mixing up of genes too. Some new combinations fall by the way side, while other quire surprising genes come to be quite common, such as the odd case of sickle cell anemia, a simple point mutation, which you would have thought would be bread out due to the higher morbiitiy and mortality of having the double dose. But the single dose confers a protection from malaria, which hides in red blood corpuscles, which then split open upon infection. Here we see a perfect example of the opposite of my thesis area, where there is no exlcusion what so ever, there is a neutral inclusion of both gene expressions. 

 I could hypothesise then that we will find that some gene alleles have one favoured all or most of the time, while others just arent important enough. Some alleles can be compensated for by other gene alleles or qausi alleles. Some gene alleles have one of the pair long term down tuned  via methylations, and that can be tissue specific. Some genes may well be turned more on at one of the pair copies. Some genes will be then later tuned or eliminated at their RNA level as far as getting stuck onto the ribosome protein factories. Sometimes we may need multiple copies of the gene on at any time to make enough protein or gene product. 

Allelic exclusuion in the context of a secually reproducing multicellular  organism is a high risk strategy in some