Tag Archives: Aristotle

A research idea yours for the taking

Why would the gene for a protein contain a part which could form amyloid (the major component of the senile plaque of Alzheimer’s disease) and another part to prevent its formation. Therein lies a research idea, requiring no grant money, and free for you to pursue since I’ll be 80 this month and have no academic affiliation.

Bri2 (aka Integral TransMembrane protein 2B — ITM2B) is such a protein.  It is described in [ Proc. Natl. Acad. Sci. vol. 115 pp. E2752 – E2761 ’18 ] http://www.pnas.org/content/pnas/115/12/E2752.full.pdf.

As a former neurologist I was interested in the paper because two different mutations in the stop codon for Bri2 cause 2 familial forms of Alzheimer’s disease  Familial British Dementia (FBD) and Familial Danish Dementia (FDD).   So the mutated protein is longer at the carboxy terminal end.  And it is the extra amino acids which form the amyloid.

Lots of our proteins form amyloid when mutated, mutations in transthyretin cause familial amyloidotic polyneuropathy.  Amylin (Islet Amyloid Polypeptide — IAPP) is one of the most proficient amyloid formers.  Yet amylin is a protein found in the beta cell of the pancreas which releases insulin (actually in the same secretory granule containing insulin).

This is where Bri2 is thought to come in. It is also found in the pancreas.   Bri2 contains a 100 amino acid motif called BRICHOS  in its 266 amino acids which acts as a chaperone to prevent IAPP from forming amyloid (as it does in the pancreas of 90% of type II diabetics).

Even more interesting is the fact that the BRICHOS domain is found in 300 human genes, grouped into 12 distinct protein families.

Do these proteins also have segments which can form amyloid?  Are they like the amyloid in Bri2, in segments of the gene which can only be expressed if a stop codon is read through.  Nothing in the cell is perfect and how often readthrough occurs at stop codons isn’t known completely, but work is being done — Nucleic Acids Res. 2014 Aug 18; 42(14): 8928–8938.

I find it remarkable that the cause and the cure of a disease is found in the same protein.

Here’s the research proposal for you.  Look at the other 300 human genes containing the BRICHOS motif (itself just a beta sheet with alpha helices on either side) and see how many have sequences which can form amyloid.  There should be programs which predict the likelihood of an amino acid sequence forming amyloid.

It’s very hard to avoid teleology when thinking about cellular biochemistry and physiology.  It’s back to Aristotle where everything has a purpose and a design.  Clearly BRICHOS is being used for something or evolution/nature/natural selection/the creator would have long ago gotten rid of it.  Things that aren’t used tend to disappear in evolutionary time — witness the blind fish living in caves in Mexico that have essentially lost their eyes. The BRICHOS domain clearly hasn’t disappeared being present in over 1% of our proteins.

Suppose that many of the BRICHOS containing proteins have potential amyloid segments.  That would imply (to me at least) that the amyloid isn’t just junk that causes disease, but something with a cellular function. Finding out just what the function is would occupy several research groups for a long time.   This is also where you come in.  It may not pan out, but pathbreaking research is always a gamble when it isn’t stamp collecting.

 

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What are prions for?

Prions existed in yeast billions of years before humanity came on the scene. Why are they still there? What are they for?  Immediately we are back in the Aristotelian world of teleology, where everything had a reason for existence and a purpose.  http://www.sparknotes.com/philosophy/aristotle/themes.html.  Teleology is simply impossible to avoid in biology. “Nothing in Biology Makes Sense Except in the Light of Evolution” is a famous quote from the magnificently named Theodosius Dobzhansky, which clothes naked teleology with respectable scientific garments.

Here’s an example of this sort of thing from back in the day.  When I was back in the Denver VA as a neurology resident dealing with the complications of immunosuppressants in Starzl’s early work on transplantation, we wondered what on earth the transplantation antigens were for.  All we knew then, is that they were important in transplant rejection. Surely they were not there to prevent cells of the same or another species from finding a new home in us.  Only later did we figure out that they were involved in antigen presentation.

A fascinating article from the first Science of the new year — http://science.sciencemag.org/content/359/6371/eaao5654 describes how the yeast organism might be using one of them (Sup35) — e.g. what the prion domains are for.  Normally the Sup35 protein functions to terminate messenger RNA (mRNA) translation into protein. However the first 123 amino acids of Sup35 can aggregate forming amyloid fibrils.  It contains a series of 9 amino acid repeats with consensus sequence PQGGYQQYN (single letter amino acid code — http://130.88.97.239/bioactivity/aacodefrm.html) which is similar to the human prion protein repeats (PHGGGWGQ).

This work showed that under a variety of stesses (energy depletion, lowering of intracellular pH) Sup35 doesn’t form amyloid-like prions, but something rather different — liquidlike spherical condensates, which subsequently solidify to form a protein gel.  Next to the prion domain is a very acidic region, important in formation of the condensate.  Low pH is seen in energy depletion, and protonates the acidic amino acids in the acidic region leading to condensate formation.   A mutated Sup35 containing only the prion domain and the acidic region will form the condensates as well in a pH dependent manner.  The condensates are far from irreversible (like prions) as they quickly disappear when the pH is raised.

If you take out the prion domain from Sup35, the catalytic region (a GTPase) in the carboxy terminal part forms irreversible aggregates — so the prion domain is in some way preventing this.

So basically the two other parts of Sup35 function to protect the business end of Sup35 from being totally put out of commission by irreversible aggregation.

The authors found that yeast cells containing Sup35 lacking the prion domain, after recovering from stress, showed impaired translational activity and a growth defect presumably because there was less functional Sup35 around. This may be what the prion domain is doing.

My guess is that the aggregation of Sup35 into actual prions has a function in yeast that we just haven’t figured out yet.

It will be interesting to see if other yeast prions (there are many) show the similar behavior (condensate formation under stress).