A Digression on Prions and the Ultimate Frame of Reference in Biological Systems


 Normal  Resident Proteins as Recognition Devices

Sup35 a yeast protein may mutate to a form which spontaneously aggregates, like-with-like, to produce amyloid-type fibrils.

A hint that potential for the bizarre may exist in sequence space is provided by "proteinaceous infectious particles" or "prions" (the vowels are transposed for euphony). This is the name given to a rare form of a normal "self" protein (originally termed "proteinaceous" since its protein nature was in doubt; Prusiner 1997).

    The rare form may appear either "spontaneously" without a mutation in the sequence of the normal protein, or as a result of a mutation in the sequence of the normal protein.

    However, the rare form has the strange property of being able to cause the normal form to change conformation to that of the rare form, so it becomes another "prion". Any property associated with the rare form, which distinguishes it from the normal form, is then acquired by what had been the normal form. These properties include

  • (i) causing more molecules of the normal form to change conformation to the rare form (i.e. each changed molecule recruits further molecules, which, in turn, recruit further molecules in an exponential manner),

  • (ii) a loss in solubility resulting in aggregation, and
  • (iii) resistance to proteases (which originally led to the idea that prions  might not be proteins; hence " proteinaceous")

    Solubility is an important protein property. As their limit of solubility is approached, molecules of a a particular protein species will tend to aggregate. This aggregation is usually correlated with a loss of function. The aggregation is protein-specific, in that proteins tend to aggregate like-with-like, leaving other protein species (of greater solubility) still in solution. 

    This property has long been exploited by biochemists to purify different protein species from mixtures by differential precipitation. Indeed, experimentally it can be shown that in a cytosol containing more than one potential prion-precursor species, seeding with a few prion molecules of one species causes conversion and aggregation only of the corresponding normal species. The other species remains soluble (Santoso et al. 2000).

    Thus one molecule of prion protein in a cell can act as a "seed", catalysing the formation of a prion aggregate. The crowded cytosol can be viewed as poised on the verge of concentration "criticality", much as a lake at sub-zero temperatures may need the addition of just one ice crystal to make the entire lake freeze (Fulton, 1982; Forsdyke 1995). The unremitting activity of molecular chaperones, which include member of the heat-shock protein family, can usually ensure that protein conformations are kept in soluble mode, so that the criticality threshold is not crossed (e.g. Warwick et al. 1999).

    Now we come to the "infectious" aspect of the name. Proteins with the prion property have been identified both in unicellular microorganisms (yeast) and organisms considered higher on the evolutionary scale. Prions transferred from individual to individual, either within a species, or between different species, can sometimes get into cells and convert (and so decrease the solubility of) the corresponding normal resident proteins, to the detriment of the organism.

    The infection may be inherited, or acquired. As far as we know, normal yeast either do not contain the abnormal prion forms or can deal with them before the exponential self-aggregation process can start (i.e. a role for molecular chaperones). When yeast cells divide, cytoplasmic contents are passed to daughter cells, so that, if the exponential process has started for some reason, any resulting change in phenotype is inherited cytoplasmically.

    As far as we know, humans do not pass prion proteins cytoplasmically in the germ line. However, a disease of cannibals in New Guinea (Kuru) was found to be caused by ingested prion protein being able to resist degradation by intestinal proteases. In this respect the acquired protein was "infectious" in that it was, like a bacterium, the agent transferring the disease from person to person.

    In some cases, the infection crosses species lines. Thus, on ingesting prion-containing meat, humans can acquire "mad cow's disease". Kuru and mad cow's disease are members of a group of diseases (not all of which are prion-based), in which neurological disfunction is associated with protein aggregation in nerve tissue.

    The prion phenomenon reveals a process by which a normal resident protein species ("self") can serve as a recognition device for an extrinsic protein ("not self") with which it shares some property. The recognition takes the form of intracellular aggregation with, in the case of prion diseases, adverse consequences for the organism. However, in principle, the phenomenon might be turned to the advantage of the organism.

    The aggregation of resident molecules can be seen as creating and amplifying a signal that a specific "non-self" protein is present, thus constituting a form of intracellular self/not-self discrimination. As a result of this recognition event, there might be a "call to arms" such  that the cell (and/or the organism) mounts a response which is adaptively advantageous. Thus, in the words of Lindquist (1997), prions may not be just "oddities in a biological freak show, but actors in a larger production now playing in a theatre near you".

    There is an analogy here with the extracellular recognition of a not-self protein ("antigen") by a resident protein ("antibody"). In this case, the resident protein has evolved for this specific purpose and, as far as we are aware, has no other purpose. In the case of intracellular proteins there appear to be no dedicated molecular species of an antibody nature. Thus proteins with some regular function in the economy of the cells may, when the conditions are appropriate, be coopted for the aggregation function. This aggregation (registering a protein as not-self) would then trigger various alarms, which would lead to responses advantageous to the organism (e.g. the interferon response, upregulation of MHC protein expression, etc.). The challenge is to try to figure how this might have come about, how it might be manifest in known phenomena, and how models for the process can be tested.

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The Ultimate Frame of Reference in Biological Systems

Note that the term "danger" is currently popular among immunologists (and it is therefore politically correct to use it in your grant applications or controversial publications). "Danger" or "dangerous" are attributes that inform us that something is potentially harmful.

    However, first a signal is recognized as emanating from a source different from "self."  This, initial "not-self" decision:

  • self or not-self?

may, in itself, prompt a response. For example, if sheep grazing in a meadow hear a sound in the wood they may move away from the wood as a precaution. They know the sound is not from one of themselves. However, once this primary not-self decision is made, another binary discrimination follows:

  • not-dangerous or dangerous?

   If not dangerous then the source is potentially friendly. If dangerous then the source is potentially unfriendly. So the source is appropriately registered as:

  • friend or foe?

   For example, if not-self displays the attribute "shepherd" (= friend) then the sheep relax. If not-self displays the attribute "wolf" (= foe) then alarms sound (bleating and running). It is true that a deaf sheep may only respond when it sees its neighbours moving. It responds, not to not-self, not to danger, but to the alarm. For the sheep collective, however, the primary event is that of self/not-self discrimination. 

    As far as bodily systems are concerned, internal "not-self" is a foe and dangerous (potentially harmful), while internal "self" is a friend and not-dangerous. Fortunately, the initial self/not-self decision usually suffices to trigger a response (alarm). Thus, attenuated or dead bacteria are sufficient to immunize. Danger, per se, does not come into the picture. Bacteria are not allowed to wander around the body, like tourists. We recognize them as "not-self," not as dangerous. And we do not require them to "break windows" (manifest their potential for harm) before we respond. 

    When what may be deemed as "self" becomes harmful, then some body component has begun to manifest not-self attributes. The yard-stick for measuring the degree of  potential for harm (dangerousness), is the degree of conversion to not-self, not the amount of damage that has already been caused. Thus, "self" is the ultimate frame of reference in a biological system.

    Self is that which is encoded in your genes at the time of your first appearance on this planet. Genes which change during your life so that different gene products are synthesized may either register as still "self" (e.g. antibody variable region genes), or register as having transformed to "not-self" (e.g. a potential oncogene). This may require very fine discrimination between "self" and "near-self", so that the latter becomes registered as "not-self."

Forsdyke, D. R. (1995) Entropy-driven protein self-aggregation as the basis for self/not-self discrimination in the crowded cytosol. J. Biol. Sys. 3, 273-287.  (Click Here)

Fulton, A. (1982) How crowded is the cytoplasm? Cell 30, 345-347.

Lindquist, S. (1997) Mad cows meet Psi-chotic yeast: the expansion  of the prion hypothesis. Cell 89, 495-498.

Prusiner, S. B. (1997) Prion diseases and the BSE crisis. Science 278, 245-251.

Santoso, A., Chien, P., Osherovich, L.Z. & Weissman, J. S. (2000) Molecular basis of a yeast prion species barrier. Cell 100, 277-288.

Warrick, J. M., Chan, H.Y.E., Gray-Board, G. L., Chai, Y., Paulson, H.L. & Bonini, N. (1999) Suppression of polyglutamine-mediated neurodegeneration in Drosophila by the molecular chaperone HSP70. Nature Genetics 23, 425-428.

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What Can We Do?

A major factor in the spread of the prion diseases is the use of the by-products (offal) of one animal to feed another. Government regulations have been drawn up to prevent this, but according to the US Office of Food and Drug Administration, (Sandra Blakeslee reports in the New York Times 11th Jan 2001):

"Large numbers of companies involved in manufacturing animal feed are not complying with regulations meant to prevent the emergence and spread of mad cow disease in the United States."

"The regulations state that feed manufacturers and companies that render slaughtered animals into useful products generally may not feed mammals to cud-chewing animals, or ruminants, which can carry mad cow disease.

    All products that contain rendered cattle or sheep must have a label that says, "Do not feed to ruminants," Dr. Sundlof said. Manufacturers must also have a system to prevent ruminant products from being commingled with other rendered material like that from chicken, fish or pork. Finally, all companies must keep records of where their products originated and where they were sold."

"Among 180 large companies that render cattle and another ruminant, sheep, nearly a quarter were not properly labeling their products and did not have a system to prevent commingling, the F.D.A. said. And among 347 F.D.A.-licensed feed mills that handle ruminant materials ... 20 percent were not using labels with the required caution statement, and 25 percent did not have a system to prevent commingling."

"Then there are some 6,000 to 8,000 feed mills so small they do not require F.D.A. licenses. They are nonetheless subject to the regulations, and of 1,593 small feed producers that handle ruminant material and have been inspected, 40 percent were not using approved labels and 25 percent had no system in place to prevent commingling."

                                                         Donald Forsdyke 2001


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This page was last edited on 06 Jul 2010 by Donald Forsdyke