The proteasome branches out

The surface of a protein is not at all like a ball of yarn, even though they are both one long string. This has profound implications for the immune system. Look at any solved protein structure. The backbone bobs and weaves taking water hating (hydrophobic) amino acids into the center of the protein, and putting water loving (hydrophilic) amino acids on the surface. So even though the peptide backbone is continuous, only discontinuous patches of it are displayed on the protein surface.

Which is a big problem for the immune system which wants to recognize the surface of the protein (which is all it first gets to see with an invading bug). Now we know that foreign proteins are ingested by the cell, chopped up by the proteasome, and fragments loaded on to immune molecules (class I Major Histocompatibility Complex antigens) and displayed on the cell surface so the immune system can learn what it looks like and react to it. The peptides aren’t very long — under 11 or so amino acids, but they are continuous.

What if the really distinct part of the protein surface (e.g. the immunogen)  is made of two distinct patches from the backbone? A fascinating paper shows how the immune system might still recognize it. Chop the protein up into fragments by the proteasome, and then have the fragments from adjacent patches put back together. You know that any enzyme can be run in reverse, so if the proteasome can split peptide bonds apart it can also join them together.

This is exactly what was found in a recent paper — Science vol. 354 pp. 354 – 358 ’16. The small peptides (containing at most 11 amino acids) finding their way to the cell surface were analyzed in a technical tour de force. In aggregate they go by the fancy name of immunopeptidome. They found that the proteasome IS actually splicing peptide fragments together. This is called Proteasome Catalyzed Peptide Splicing (PCPS). The present work shows that it accounts for 1/3 of the class I immunopeptidome in terms of diversity and 1/4 in terms of abundance. One-third of self antigens are represented on the cell surface of the immune cell line they studied (GR-LCL the GR-lymphoblastoid cell line) ONLY by spliced peptides. The ordering of the spliced peptide was the same as the parent protein in only half. There was no preference for the length of the protein skipped by the splice.

The work has huge implications for immunology, not least autoimmune disease.

So today I wrote the author the following

Dr. Mishto

Terrific paper ! Do you have any evidence for the spliced peptides being spatially contiguous on the surface of the parent protein. Have you looked?

This makes a lot of sense, because the immune system should ‘want’ to recognize protein conformations as they exist in the living cell, rather than stretches of amino acid sequence in the parent protein. Also, with few exceptions the surface of a given protein in vivo is a collection of discontinuous peptide sequences of the parent protein. I’ve always wondered how the immune system did this, and perhaps your paper explains things.


and got this back almost immediately

Dear Luysii

Interesting idea. We shall have a look for few examples where the crystallography structure or the parental protein is disclosed already.



It doesn’t get any better than this. Tomorrow I will be exactly 78 years and 6 months old. It shows I can still think (on occasion).

Addendum 17 Nov ’16;  It looks as though proteins are fed into the central cavity of the proteasome as a completely denatured single strand.  See figure 5 of PNAS 113 pp 12991 -m12996 ’16.  The channel to get in appears quite narrow.

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  • YoYo  On October 26, 2016 at 11:14 pm

    Thanks for writing this blog. I learn so much here about the frontiers of biochemistry.

    This is a huge discovery for autoimmune diseases. I never could understand how the thymus gland could let through the highly polyclonal immune cells that attack in diseases like Type 1 diabetes and rheumatoid arthritis.

    Obviously we would expect the occasional low-affinity antibody that is suddenly expressed at high levels in response to an infection, like the anti-AchR antibodies in myasthenia gravis. They’re not sticky enough for the thymus to weed them out, but a flood of them can cause problems. Doing the math of billions of antibody clades and a several orders of magnitude pop in levels during an infection, it is obvious that a single random self protein will be attacked once in a blue moon.

    But that can never explain the huge variety of antibodies that start sticking during a major inflammatory disease. Such a thing as an anti-nuclear antibody (ANA) test would not even be possible with such “lottery antibodies”. The ANA test depends on a torrent of broad spectrum autoantibodies. Nor could it explain the predilection for certain tissues but not others.

    It all falls into place if protein fragment splicing exists and can be triggered by inflammation. Something happens to a few cells to start inflammation. Then the cells start promiscuously splicing fragments that draw in more immune cells. The resulting inflammation triggers the neighbors to start promiscuously splicing fragments and presenting them to the immune system, spreading the effect to its neighbors. Gradually the cascade expands to the entire tissue. Eventually the adaptive immune system has a lot of activated cells against a wide variety of splice variants, allowing it to attack the main proteins of a particular tissue. Boom, rheumatoid arthritis.

    Let’s put some numbers on it: 22,000 genes * (1000 fragments per gene)^2 = 22 billion MHC-advertised epitopes. The squaring is an estimate of the combinatorial explosion of the number of ways the fragments can be spliced. If I remember right, the adaptive immune system has only about a billion possible antibodies. Therefore promiscuous splicing can explore a significant part, if not all, of the space of antibody clades.

    In a few years there is a good chance that inflammatory disorders can be put into remission with a single depot injection of splice inhibitor, anti-inflammatory like methotrexate, and maybe a cytokine inhibitor. I hope so, as someone with three cases of rheumatoid arthritis and two cases of inflammatory bowel disease in my family history.

  • luysii  On October 27, 2016 at 9:26 am

    Interesting idea, but if the proteasome is doing the splicing by reversing its protease activity (as mentioned) inhibiting it would have all sorts of untoward consequences

  • Melchizidek  On November 4, 2016 at 11:37 am

    This is phenomenal. Great thinking and sleuthing!

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