Category Archives: Molecular Biology

Amyloid structure at last !

As a neurologist, I’ve been extremely interested in amyloid  since I started in the late 60s.  The senile plaque of Alzheimers disease is made of amyloid.  The stuff was insoluble gunk. All we had back in the day was Xray diffraction patterns showing two prominent reflections at 4 and 9 Angstroms, so we knew there was some sort of repetitive structure.

My notes on papers on the subject over the past 20 years contain  about 100,000 characters (but relatively little enlightenment until recently).

A while ago I posted some more homework problems — https://luysii.wordpress.com/2021/09/30/another-homework-assignment/

Homework assignment #1:  design a sequence of 10 amino acids which binds to the same sequence in the reverse order forming a plane 4.8 Angstroms thick.

Homework assignment #2 design a sequence of 60 amino acids which forms a similar plane 4.8 Angstroms thick, such that two 60 amino acid monomers bind to each other.

Feel free to use any computational or theoretical devices currently at our disposal, density functional theory, force fields, rosetta etc. etc.

Answers to follow shortly

Hint:  hundreds to thousands of planes can stack on top of each other.

 

If you have a subscription to Cell take a look at a marvelous review full of great pictures and diagrams [ Cell vol. 184 pp. 4857 – 4873 ’21 ].

 

Despite all that reading I never heard anyone predict that a significantly long polypeptide chain could flatten out into a 4.8 Angstrom thick sheet, essentially living in 2 dimensions.  All the structures we had  (alpha helix, beta pleated sheet < they were curved >, beta barrel, solenoid, Greek key) live in 3 dimensions.

 

 

So amyloid is not a particular protein, but a type of conformation a protein can assume (like the structures mentioned above).

 

 

So start with NH – CO – CHR.  NH  CO and C in the structure all lie in the same plane (the H and the side chain of the amino acid < R >  project out of the plane).

 

Here’s a bit of elaboration for those of you whose organic chemistry is a distant memory.  The carbon in the carbonyl bond (CO) has 3 bonding orbitals in one plane 120 degrees apart, with the 4th orbital perpendicular to the plane — this is called sp2 hybridization.  The nitrogen can also be hybridized to sp2.  This lets the pair of electrons above the plane roam around moving toward the carbon.  Why is this good?  Because any time you let electrons roam around you increase their entropy (S) and anything increasing entropy lowers their free energy (F)which is given by the formula F = H – TS where H is enthalpy (a measure of bond strength, and T is the absolute temperature in Kelvin.

 

 

So N and CO are in one plane, and so are the bonds from  N and C to the adacent atoms (C in both cases).

 

You can fit the plane atoms into a  rectangle 4.8 Angstroms high.  Well that’s one 2 dimensional rectangle, but the peptide bond between NH and CO in adjacent rectangles allows you to tack NH – CO – C s together while keeping them in a 3 dimensional parallelopiped 4.8 Angstroms high.

 

 

Notice that in the rectangle the NH and CO bonds are projecting toward the top and bottom of the rectangle, which means that in each plane  NH – CO – CHR s, the NH and CO are pointing out of the 2 dimensional plane (and in opposite directions to boot). This is unlike protein structure in which the backbone NHs and COs hydrogen bond to each other.  There is nothing in this structure for them to bond to.

 

 

What they do is hydrogen bond to another 3 dimensional parallelopiped (call it a sheet, but keep in mind that this is NOT the beta sheet you know about from the 3 dimensional structures of proteins we’ve had for years).

 

 

So thousands of sheets stacked together form the amyloid fibril.

 

Where does the 9 Angstrom reflection of cross beta come from?  Consider the  [ NH – CHR – CO ]  backbone as it lies in the 4.8  thick plane (I never thought such a thing would be even possible ! ).  It curves around like a snake lying flat.  Where are the side chains?  They are in the 4.8 thick plane, separating parts of the meandering backbone from each other — by an average of 9 Angstroms

 

Here is an excellent picture of the Alzheimer culprit — the aBeta42 peptide as it forms the amyloid of the senile plaque

 

 

You can see the meandering backbone and the side chains keeping the backbone apart.

 

 

That’s just the beginning of the paper, and I’ll have lots more to say about amyloid as I read further.   Once again, biology instructs chemistry and biochemistry giving it more “things in heaven and earth, Horatio, than are dreamt of in your philosophy.”

The most interesting paper I’ve read this year

We all know what the estrogen receptor is and what it does.  It’s a large protein with 3  functional components.  Actually there are several estrogen receptor proteins, but I’m going to discuss just one — Estrogen Receptor alpha (ERalpha).

Here are the components:

a DNA binding domain (which binds to stretches of bases called the Estrogen Response Element (ERE))

a domain which binds estrogen changing the conformation of the third domain which is —

a domain which binds to RNA polymerase II activating it so it transcribes genes into mRNA.

Given the complexity of the hormonal cycles, it is far from surprising that the estrogen receptor controls the levels of 15% of all annotated protein coding genes < Cell vol. 145 pp. 622 – 634 ’11 >.

Given its importance in breast cancer, ERalpha has been intensively studied for years.

Now various regions of proteins have been assigned function, the SH2 domain binds to phosphotyrosine in proteins, SH3 binds to proline rich motifs, RNA Binding Domains (RBDs) bind to (what else?) RNAs.  Each of them has a characteristic sequence of amino acids allowing them to be picked out from DNA sequences.

Enter Cell vol. 184 pp. 5086 – 5088, 5215 – 5229 ’21 where ERalpha was found to bind to over 1,200 messenger RNAs (mRNAs).   It was not supposed to do that as it doesn’t contain any RBDs (well at least the RBDs we knew about — back to the drawing board on that one).  Even more interesting is the fact what most of the mRNAs bound by ERalpha aren’t from the genes whose ERE ERalpha binds.

Life is said to have originated in the RNA world.  We all know about the big 3 important RNAs for the cell, mRNA, ribosomal RNA and transfer RNA.  But just like the water, sewer, power and subway systems under Manhattan, there is another world down there in the cell which doesn’t much get talked about.  These areRNAs, whose primary (and possibly only) function is to interact with other RNAs.

The RNA world is still alive and well in all our cells.  It’s like DOS still out there under Windows, or Unix and its command line under the Apple interface. We studied proteins and DNA because they were (relatively) easy to study.

The papers go on to study how ERalpha RNA binding affects cancer (which it does).

But there are far larger questions the work brings forth.

l. ERalpha is just one nuclear hormone receptor and Estrogen is just one hormone.  Do the nuclear hormone receptor for other hormones also bind RNA? Have we been missing some of their actions inside cells and if so there are mechanisms to exploit?

2. Why stop at nuclear hormone receptors?  ERalpha binds RNA with no RNA binding  domains (RBDs) in sight.  Do other proteins also bind RNAs and if so what does it mean?

Fantastic stuff.  There is a whole world of possibilities opening before our eyes thanks to these papers.

It reminds me of what an anatomy professor told us when we were studying neuroanatomy — ‘unfortunately everything is connected to everything else’.

Ubiquitination isn’t just for proteins

Time to look up from the plow biochemists.  Everyone knows that ubiquitin is added to proteins to destroy them.  The carboxy terminal amino acid of ubiquitin (glycine) forms an amide with the epsilon amino acid of a lysine called an isopeptide bond, and off  the protein goes to the proteasome for destruction.  This is simplistic and ubiquitination has many other other roles in the cell, but there isn’t time for it here.

I couldn’t resist putting in two interesting facts about ubiquitin.

#1. Like sharks,  evolution hasn’t changed ubiquitin much — only 3/71 amino acids differ between yeast and us.

#2 Ubiquitin is so stable that boiling water doesn’t denature it < Science vol. 365 pp. 502 – 505 ’19 >.

We have over 600 E3 enzymes (ubiquitin ligases), 40 E2 enzymes, and 8 E1 enzymes, and all 3 types are required to add ubiquitin to proteins.

Once a bacterium gets inside a cell, one of the ways the innate immune system attacks it is by ubiquitinating its proteins.  Nothing out of the ordinary there.

Salmonella (the organism responsible for most cases of food poisoning) is one such.  Our cells ubiquitinate the hell out of it.  However Nature vol. 594 pp. 28 – 29, 111 – 116 ’21 shows that, not just Salmonella proteins are the only sites of ubiquitination.  We also ubiquitinate endotoxin (lipopolysaccharide) which is a combination of sugars and lipids, with nary an amino acid in sight.  Endotoxin is a component of the outer membrane of every Gram negative bacterium, so the effect is likely not confined to Salmonella.

Even more spectacular is the enzyme adding ubiquitin.  It is called RNF213 (aka Mysterin), which looks like nothing the classic E3 enzymes we know and love.  For one thing in addition to E3 activity, it has a motor domain, a zinc binding domain and other domains of unknown function.  It’s a real monster with 5,184 amino acids and a molecular mass of 584 kiloDaltons.

There is a lot of interesting molecular biology to RNF213 — mutations cause Moya moya disease.

But the papers are particularly interesting because they show a lot of work of a new type needs to be done.

What else does Mysterin ubiquitinate?  Are there other enzymes in the cell adding ubiquitin, and if so, what do they ubiquitinate?

Definitely time to expand the well plowed field of ubiquitin.

Frameshifting

It is a pleasure to get back to the science after the ugly real world intruded with

l. A president in early dementia — https://luysii.wordpress.com/2021/06/30/biden-is-in-early-dementia-the-evidence/

2. The latest in politically correct racism  — https://luysii.wordpress.com/2021/07/03/hitler-would-have-loved-it/

but these things needed to be addressed.

I was very pessimistic about the chance of a vaccine for the pandemic based on my experience with AIDS/HIV1.  Why? Because no vaccine for HIV1 has been forthcoming despite 40 years of intense effort.  I am delighted to be wrong about pandemic vaccines.

But AIDS isn’t the kiss of death it was when I was in practice back in the 80s.  Why?  Because we know so much about what happens after the virus infects cells.  We attack all it’s weak points, from its genome, its reverse transcriptase.  So AIDs is now a chronic manageable disease.

So the more we know about SARS-Cov-2 the more ways we’ll find to attack it.   Which brings me to Science vol. 372 pp. 1306 – 1313 ’21.

The pandemic virus SARS-CoV-2 (and all coronaviruses) use something called frameshifting.

Here is a brief tutorial

Her fox and dog ate our pet rat

H erf oxa ndd oga teo urp etr at

He rfo xan ddo gat eou rpe tra t

The last two lines make no sense at all, but (neglecting the spaces) they have identical letter sequences.

Here are similar sequences of nucleotides making up the genetic code as transcribed into RNA

ATG CAT TAG CCG TAA GCC GTA GGA

TGC ATT AGC CGT AAG CCG TAG GA.

GCA TTA GCC TAA GCC GTA GGA ..

Again, in our genome there are no spaces between the triplets. But all the triplets you see are meaningful in the sense that they each code for one of the twenty amino acids (except for TAA which says stop). ATG codes for methionine (the purists will note that all the T’s should be U). I’m too lazy to look the rest up, but the ribosome doesn’t care, and will happily translate all 3 sequences into the sequential amino acids of a protein.

Both sets of sequences have undergone (reading) frame shifts. The examples are of +1 and +2 frameshifts.

SARS-CoV-2 uses a -1 frameshift.  this is necessary for the synthesis of nonstructural protein 12 (nsp12), crucially important to the virus as it codes for the viral RNA dependent RNA polymerase.

To produce the frameshift, the virus actually throws a monkey wrench at the ribosome.  At the site of the future frameshift the viral genome forms a pseudoknot  (https://en.wikipedia.org/wiki/Pseudoknot) which blocks the smooth translation of the ribosome along the viral genome, then it backs up by 1 (the -1 frameshift) and chugs on.

So PNAS vol. 118 32023051118 ’21 threw the kitchen sink (e.g. every compound they could think of) at the virus to find one which stopped the frameshift and they found one: merafloxacin a fluoroquinolone.  There are all sorts of fluoroquinolones in use as antibodies, so it’s time to try the others out.

This is unlikely to be a general approach to coronavirus therapy, as the RNA sequence at the frameshift site is likely to be different in each coronavirus.

I don’t think frameshifting occurs in eukaryotic cells, but I’m not sure.  Does anyone out there know?

 

Another virus escapes from a lab

Given the excitement over the possibility that the pandemic virus (SARS-CoV-2) escaped from a lab in Wuhan, it’s time to shamelessly republish a clairvoyant science fiction story of mine first published 19 November 2019.

A science fiction story (for the cognoscenti) — answer to the puzzle and a bit more

Comrade Chen we have a serious problem.

Don’t tell me one of our bugs escaped confinement.

Worse.  One of theirs did.  And it’s affecting the PLA (People’s Liberation Army).  Some are turning into pacifists.

It doesn’t kill them?

No. But for our purposes it might as well.

It’s a typical adenoassociated virus (AAV) like we use.

Well, what does the genome look like?

We’ve sequenced it and among other things, it codes for a protein which enters the brain and alters behavior.

What?

Well, the enemy has some excellent biologists, one of whom works on Wolbachia.

What’s that?

It’s a rickettsial organism which changes the sex life of some insects.

I don’t believe that.

Do you have a cat?

Yes.

Well many cats contain another organism (toxoplasma gondi).

So what.

Rats infected by the organism become less afraid of cats.

Another example please.

A fungus infecting carpenter ants causes the ant to leave its colony, climb a tree, chomp down on the underside of a leaf and die, freeing fungal spores to fall on the ground where they can reinfect new ants.

Well what is the genome of the virus?

It has some very unusual sequences, and one which proves that the Wolbachia biologist on the other side has a very large ego.

How so.

Well in addition to the brain infecting protein, there is a very unusual triplet of peptides all in a row.

Methionine Alanine Aspartic Acid Glutamic acid, then a stop codon, then Isoleucine Asparagine, than a stop codon, then Threonine Alanine Isoleucine Tryptophan Alanine Asparagine.  We think that the first two in some way cause readthrough of the stop codons so the protein following the short peptides is made.

Where does the big ego come in?

Sir, proteins can have hundreds and hundreds of amino acids.  People got tired of writing their full names out, so each of the 20 amino acids was given a single letter to stand for it.

M – Methionine

A – Alanine

D – Aspartic acid

What does D have to do with Aspartic acid?

Nothing sir, look on the letters as Chinese characters.

E -Glutamic Acid

I – isoleucine

What about the stop codon between Glutamic acid and Isoleucine

Just regard it as a space.

N – Asparagine

Nooo! ! ! I I’m beginning to get the picture.

Yes sir, it stands for MADE IN TAIWAN

—-

A few years later

Well the Taiwanese biologist outsmarted himself (or herself).   The Taiwanese soldiers wouldn’t fight either as the virus spread.  Most conflicts between nation states pretty much ended (Russia/Ukraine, North Korea/South Korea) etc. etc.  The Taiwanese biologist was nominated for the Nobel Peace Prize, and did receive it in absentia, as every military type in the world was looking for him (or  her), so he (or she) went into hiding, and is believed to be living in an Ashram near Boulder, Colorado.

Unfortunately, the idea of using viruses to change human behavior spread past nation states, and private groups with their own agendas began using it.

The ‘new soviet man’ of the previous century looked rather benign compared to what subsequently happened.

The next story for the scientific cognoscenti will describe the events leading up to the impeachment trial of President Jon Tester in 2028.

Ashkenazi Jews are extremely inbred

Neurologists are inherently interested in  psychosis, not least because too much dopamine in the form of L-DOPA can trigger it.  I’ve always found it remarkable that dopamine blocking agents (phenothiazines, and most antipsychotics) can attack psychotic thought itself.  This is much more impressive to me than the ability of other drugs (alcohol, coffee, marijuana, cocaine) to affect mood.

So it’s always worthwhile to read another paper about the genetics of schizophrenia, a very hereditary disease.  All the risk factors we’ve found by GWAS (Genome Wide Association Studies) account for at most of 1/3 of genetic risk in schizophrenia.  For details please see https://luysii.wordpress.com/2014/08/24/tolstoy-rides-again-schizophrenia/.

So I was interested in another crack at finding more genetic causes of schizophrenia  [ Neuron 109, 1465–1478, May 5, 2021 ].  As often happens, the most interesting thing in the paper was something totally tangential  to my original interest in it. 

Here it is —   ”  For example, the Ashkenazi Jewish (AJ) population, currently numbering >10 million individuals world- wide, effectively derives from a mere 300 founders 750 years ago ” (Carmi et al., 2014;Nat. Commun. volume 5, 4835.).  

I find this assertion incredible.  But, as explained below, there is pretty good evidence (although subtle and quite technical) that it’s correct.

Ashkenazi Jews are those previously found only in Europe and the Americas, as opposed to Sephardic Jews, previously found only in the mideast and Africa.  Both are now found in Israel.  Ashkenazi Jews were chosen for the study because any deleterious genes producing schizophrenia  present in the original 300 wouldn’t have been washed out by natural selection in just 30 generations in 750 years. 

The Ashkenazim make the inbreeding among French Canadians look like pikers — a population of 2 million derived from a founder population of 9000 people over the next 170 years — for details please see https://luysii.wordpress.com/2019/07/17/the-wages-of-inbreeding/.  Note that neither population tried to inbreed, it’s just that there was no one else geographically available to breed with for the French Canadians, and no one else culturally available for the Ashkenazi’s.  

At least with the French Canadians we have immigration records to tell us how large the founder population was.  How sure are we about the 300 strong founder population of present day Ashkenazi Jews?  We’re not and I’m not even though it was published in a peer reviewed reputable journal.  There is a lot of guesswork in figuring out just how large a genetic bottleneck is.  It all depends on the model used, and I don’t trust models in general.  I’ve seen too many crash and burn. (For details — https://luysii.wordpress.com/2019/03/03/i-mistrust-models-2/)

However, the Neuron paper contains a reference to another paper which provides excellent empiric evidence for a small founder population, (PLoS Genet. 14, e1007329. 2018).  Here’s a direct quote.  It’s quite a mouthful; I’ll try to explain below the quote what the terms mean, because I think many nonscientific types are likely to be interested in the idea that Ashkenazi Jews are that inbred. 

Just skip the paragraph if it’s incomprehensible, go to *** and read the explanatory material, and then read the paragraph again. 

“We estimate that 34% of protein-coding alleles present in the Ashkenazi Jewish population at frequencies greater than 0.2% are significantly more frequent (mean 15-fold) than their maximum frequency observed in other reference populations. Arising via a well-described founder effect approximately 30 generations ago, this catalog of enriched alleles can contribute to differences in genetic risk and overall prevalence of diseases between populations.”

****

Explanatory material.

Our genetic material (DNA) is made of 4 different compounds A, T, G, C (called nucleotides) which are linked together in chromosomes.  The order is crucial, just as the order of letters in a word is crucial for meaning (consider united and untied).  So how many slots for the nucleotides are there in our genome ? Just 3,200,000,000.  Just as combinations of dots and dashes code for letters in Morse code, combinations of  3 nucleotides code for the 20 amino acids that make up proteins. 

Proteins are big.  For instance, the protein  (beta-globin)mutated in sickle cell anemia contains 146 amino acids, and all it takes to produce the disease is a switch from one amino acid to another at position six.  The other 145 amino acids in the chain are unchanged. So sickle cell beta globin with a change in its nucleotide sequence is an allele (alternate form) of normal beta globin.  

Every population of people contains alleles of every protein.  Some are common (over 5% of the population showing them), but most are rare.The PLoS paper looked at  73,228 alleles of all 20,000 or so proteins that we have in our genome (yes technology now can do these sorts of things) in the general population.  The authors looked at the alleles in the Ashkenazi population which were present at greater than 1/500 (.2%).  Then they looked at the frequency of the same allele in several other non-Ashkenazi population (about 5000 each of non-Finnish Europeans, African Blacks and Latinos), and found that these alleles occurred15 times less frequently (on average).   So Ashkenazi’s have alleles that are lots more common than in other populations.  Actually it’s more than some, because about 1/3 of the alleles they studied are an average of 15 times as common.

What does this mean?  It means that when a small founder population with a rare allele becomes ‘fruitful and multiplies’, the rare allele will multiply right along with it and not be lost by outbreeding (which was certainly true of the Ashkenazis for 600 of the last 750 years).

Now read the paragraph in bold above again. 

This is the evidence that current day Ashkenazi’s come from a very small founder population.  It’s pretty good.  I hope that I’ve made this somewhat comprehensible;  if not, please write a comment.

Is there anything in the cell that has just one function — more moonlighting — this time mRNA

Able was I ere I saw Elba said Napoleon. It’s called a palindrome, and can be read either way. So can DNA which brings me to antisense transcription of DNA, particularly in two famous retroviruses –the AIDS virus (HIV1) and HTLV-1.  

Proc. Natl. Acad. Sci. vol. 118 e2014783118 ’21  shows that mRNA can moonlight to do other things than code for protein.  Here’s a direct quote to set the stage.

“Retroviruses share a similar genome structure. The integrated retroviral genome, called the provirus, has two identical long terminal repeats (LTR) located at its 5′ and 3′ ends, respectively. The 5′ LTR acts as the promoter of almost all retroviral genes and thus is indispensable for viral transcription and replication. However, selective methylation of the 5′ LTR and the subsequent viral latency have been observed in HIV-1 and HTLV-1. In contrast, the 3′ LTR of HIV-1 and HTLV-1 remains nonmethylated, and recent findings have shown that novel retroviral genes are transcribed from the 3′ LTR in an antisense direction”.

The 3′ LTR of the AIDS virus enables antisense transcription for  the unimaginatively named ASP (AntiSense Protein).  So the mRNA for ASP is transcribed in the nucleus.  But it doesn’t get out as well as it might, because its 5′ end isn’t polyAdenylated.  So it sticks around in the nucleus and binds to DNA, turning off transcription of the regular HIV1 genome — e.g. helping to maintain viral latency (and preventing a true cure of HIV1 in any individual).

This is unprecedented.  Here is an mRNA with a completely different function (e.g. regulating gene expression).  This is classic moonlighting as something else and the authors call the mRNA for ASP a bifunctional mRNA. 

The other, retrovirus HTLV-1 also has an antisense transcript making a protein called HBZ (your don’t want to know what it stands for). Unlike ASP, HBZ turns on a variety of genes. 

I’ve been fascinated by moonlighting molecules, probably because they show the depths of our ignorance of the biochemical machinations inside the cell.  Even when you think you’ve got the function of a molecule tied down, it goes off and does something else. 

 Here are some links to other posts on the subject.  To get to them just click on the titles

Moonlighting molecules

More moonlighting

A moonlighting quorum sensing molecule

A moonlighting quorum sensing molecule

Bacteria talk to each other using quorum sensing molecules. Although the first one was found 50 years ago, the field really opened up with the work of Bonnie Bassler at Princeton in the 90s. These are small molecules which bacteria secrete, so that when there are a lot of bacteria around, the concentration of quorum sensors rises, allowing them to get into bacteria (by the law of mass action) changing gene expression for a variety of things, particularly virulence and biofilm formation. They have also been used by bacteria to compete with those of a different species.  There was a lot of hope, that we could control some nasty bugs (such as Pseudomonas) by messing about with their quorum sensors, but it hasn’t panned out. 

The real surprise came in a paper [ Proc. Natl. Acad. Sci. vol. 118 e2012529118  ’21 ]showing that Pseudomonas uses one of its quorum sensing molecules (C12 < N-3-oxo-dodecanoyl) homoserine lactone > ) inside the eukaryotic cells it attacks. 

What it does once inside, is to attack a cellular organelle I’ve (and probably you) never heard of called vaults.  They’s been known since ’86, and given their size (12.9 megaDaltons) I’m surprised I’d never heard of them.  The likely reason is that no one knows what their function is. 

It is made of just 3 proteins

l. MVP — Major Vault Protein, mass 100 kiloDaltons 96 copies/vault

2. VPARP — Vault poly ADP ribose polymerase 190 kiloDaltons

3. Telomerase associated protein 290 kiloDaltons.

Human vaults contain 4 different RNAs (called, naturally enough vault RNAs < vtRNAs >).  They are 88 – 100 nucleotides long.  

Vaults look like a hand grenades and are 670 Angstroms long and 400 Angstroms in maximum diameter. 

[ Cell vol. 176 pp. 1054 – 1067 ’19 ] says that there can be 10,000 to 100,000 vaults/cell.  So why haven’t I seen them?

One of the vtRNAs binds to a protein involved in autophagy inhibiting it. This is an example of an RNA binding to a protein altering its function, something unusual until you think of the ribosome or the spliceosome. Starvation decreases the number of vaults inducing autophagy.

Once pseudomonas C12 gets into a cell it binds to the Major Vault Protein, causing its translocation into lipid rafts, the net effect being attenuation of the p38 protein kinase pathway to attenuate programmed cell death (apoptosis).  

So C12 keeps the cell alive when normally it would die.  A lot of recent work has shown that bacteria infiltrate cancers.  Do they do something similar to cancer cells to keep them alive. 

It really makes you humble (or should) to realize how many separate parts of cellular and molecular biology you must understand to even hope to understand how cells (and bacteria) go about their business. 

Think of how many terms were introduced to understand what the humble quorum sensor C12 is up to. 

Do glia think? Take II

Do glia think Dr. Gonatas?  This was part of an exchange between G. Milton Shy, head of neurology at Penn, and Nick Gonatas a brilliant neuropathologist who worked with Shy as the two of them described new disease after new disease in the 60s ( myotubular (centronuclear) myopathy, nemaline myopathy, mitochondrial myopathy and oculopharyngeal muscular dystrophy).

Gonatas was claiming that a small glial tumor caused a marked behavioral disturbance, and Shy was demurring.  Just after I graduated, the Texas Tower shooting brought the question back up in force — https://en.wikipedia.org/wiki/University_of_Texas_tower_shooting.

Well that was 55 years ago, and we’ve learned a lot more about glia since.  

If glia don’t actually think, they may actually help neurons think better.  Since the brain is consuming 20% of your cardiac output as you sit there, it had better use the energy in the form of glucose  brought to it efficiently, and so it does, oxidizing it using oxygen (aerobic metabolism).  Glia on the other hand for reasons as yet unknown oxidize glucose anaerobically producing lactic acid (aerobic glycolysis). They transport the lactic acid to neurons and blocking transport impairs memory consolidation in experimental animals.  In fact aerobic glycolysis occurs in conditions of high synaptic plasticity and remodeling.  

The brain is 60% fat, some of which is cholesterol, which has to be made in the brain, as it doesn’t cross the blood brain barrier. Although neurons can synthesize cholesterol from scratch, most synthesis of cholesterol in the brain occurs in astrocytes.  It is than carried to neurons by apolipoprotein E.  As you are doubtless aware, apolipoprotein E (APOE) comes in three flavors 2, 3 and 4, and having two copies of APOE4 increases your risk of Alzheimer’s disease. 

But APOE does much more than schlep cholesterol to neurons according to a recent paper [ Neuron vol. 109 pp. 907 – 909, 957 – 970 ’21 ] Inside the particles are microRNAs.  You’ll recall that microRNAs decrease  the expression of proteins they target by binding to the messenger RNA (mRNA) for the targeted protein triggering its destruction. 

The microRNAs inside APOE suppress enzymes involved in de novo neuronal cholesterol biosynthesis (why work making cholesterol when the astrocyte is giving to you for free?).

This is unprecedented.  Passing metabolites (lactic acid, cholesterol) to neurons is one thing, but changing neuronal protein expression is quite another. 

Passing microRNAs in exosomes has been well worked out between cells (particularly cancer cells) outside the brain, but that’s for another time.