Tag Archives: EZH2

The Dr. Jekyll and Mr. Hyde protein

If there ever was a protein with a Dr. Jekyll and Mr. Hyde character (https://en.wikipedia.org/wiki/Dr._Jekyll_and_Mr._Hyde_(character))it is EZH2, a protein whose function we thought we knew.

EZH2 is an enzyme which puts methyl groups on lysine #27 of histone H3 (forming H3K27Me3).     So as good chemists that tells you that it removes the positive charge usually found on the amine group lysine at physiological pH.  But chemistry is helpless here unless you know what histone H3 does.  Addendum 27 July — clearly I’m not a good chemist when I write late at night.  Ashutosh points out that the positive charge on nitrogen at physiologic pH remains even when one, two or all the hydrogens are replaced by methyl groups.  Acetylation of the amino group of lysine removes the positive charge.  The methylation of lysine #27 is just one part of the histone code allowing other proteins to specifically bind here. As of 2013 some 130 different post-translational histone modifications were known.  

The DNA in each of our cells is just over a yard long.  To fit inside it must be compacted down.  4 different histone proteins get together to form an octomer around which DNA wraps in nearly two complete turns, compacting DNA down by a factor of ten.  The details of the further compaction have been studied for 50 years and are still under debate.

You’d think that the methylation of lysine #27 and loss of the positive charge would make it less likely to bind to the negative phosphates of the DNA chain.  This should free up the DNA so it can be transcribed to RNA and make proteins.

That’s not at all what happens. There are other proteins which bind H3K27Me3 and compact the DNA down so it becomes inactive (unable to be transcribed into mRNA).

Well that was the state of play until Proc. Natl. Acad. Sci. vol. 117 pp. 16992 – 17002 ’20.  So much for Dr. Jekyll.

Some forms of cancer activate kinase enzymes (AKT, JAK3) which place phosphates on serine #21 or tyrosine #244 of EZH2 respectively.   This causes a giant structural arrangement of amino acids #135  to #195.  Now the protein interacts with another enzyme p300 (a histone acetyl transferase) whose net effect is to UNcompact DNA and activate gene transcription.  Even worse, the transcription products of the genes help the cancer along.  Definitely Mr. Hyde.

This is a radically different function for EZH2 and you have to wonder how many other proteins lead double lives like EZH2.

The classic examples of a huge structural shift in a protein complex are the spike proteins of viruses (notably SARS-CoV-2), which unfold to form a needle piercing a cell allowing injection of the viral genetic material. Here are some nice pictures of the fusion protein of influenza virus in action — http://faculty.washington.edu/kklee/Influenza_SAXS.html.  But this is structural change in pursuit of a known physiological effect.

The double life of EZH2 is remarkable.   Some proteins have more than one effect in the cell — this is called moonlighting.  One example is cytochrome c, which is normally found in the intermembrane space of the mitochondrion where it is involved in electron transport.  When it is released into the cell cytoplasm due to mitochondrial damage, the cell quietly kills itself (apoptosis) — definitely a moonlighting function.  But the structure of cytochrome c doesn’t change to accomplish this, just its location.

Fascinating stuff, and the paper should be read to see just how profound the shift in structure that EZH2 undergoes actually is.

This is just a small window into the intricacy (and beauty if you will) of the cellular and biochemical events underlying our existence.  There is far more to discover, so stay tuned.

For some further musings on this point — https://luysii.wordpress.com/2009/09/17/the-solace-of-molecular-biology/

Junk that isn’t

The more we understand, the more we realize how little we’ve understood what we thought we understood.   Here is a double example.

We have 1,400,000 Alu elements in our genome.  They are about 300 nucleotides long, meaning that there is over 1 every 3,000 nucleotides in our 3,200,000,000 nucleotide genome.  They don’t code for protein, and were widely thought to be junk, selfish genes whose only role was to ensure that the organism carrying them, kept them along as they reproduced.

This post contains a heavy dose of contemporary molecular biology.  If you’re a little shaky on some of it have a look at — https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/ — and follow the links.

Not so says Proc. Natl. Acad. Sci. vol. 117 pp. 415 – 425  ’20.  They are part of several important physiologic processes (1) T lymphocyte activation (2) heat shock stress (3) endoplasmic reticulum stress.  All 3 cause transcription of Alu’s by RNA polymerase III (pol III).

All RNA levels increase with heat shock, including RNAs made from Alu elements.  They bind directly and tightly (nanoMolar affinity) to RNA polymerase II (which transcribes protein coding genes) and co-occupy the promoters of repressed genes, preventing transcription of these genes and protein synthesis of them.  At least that was the state of play 11 years ago (PNAS 105 5569 – 5574 ’09)

This paper notes that Alu is not passive, but actually a self-cleaving ribozyme (an enzyme made of RNA), an entirely new role.  When complexed with another protein EZH2 (a polycomb protein thought to be a transcriptional repressor using its lysine methylation activity), the rate of Alu self-cleavage increases by 40%.

So what?

In addition to stoping transcription, Alu also retards transcription elongation.  So stress increases in EZH2 causes Alu to cleave itself faster, turning off  repression and improving the responses to the 3 types of stresses above.

So we really didn’t understand both Alu which has been studied for years, or EZH2 a polycomb protein (ditto).  Alu is a self-cleaving ribozyme, and EZH2 doesn’t just turn off genes by its enzymatic activity (lysine trimethylation), but binds to an RNA so it can cleave itself faster (e.g. its a cofactor).

Fascinating and humbling to see how much there is to know about things we thought we knew.  But it’s also exciting.  Who knows what else is out there to discover about the known, never mind the known unknowns.