New study uncovers multiple effects of little-known DNA repair protein

By Dr. Liji Thomas, MDDec 2 2019

Injury and repair are part of the normal life cycle of any tissue or organ in the human body. However, if macroscopic tears or breaks occur in the bones or joints, for instance, the effects are immediately perceptible. Not so with chromosomes, which contain the DNA of life. Both extremely valuable and extremely fragile, DNA is the focus of highly efficient repair proteins.

Now a new study shows a new function for one of these lesser-known proteins called HMCES (pronounced Hem'-sez). The study, which was published in the journal Molecular Cell, on Dec. 2, 2019, shows that when mouse lymphocytes lack this protein, they fail to carry out DNA recombination and this in turn makes it impossible to produce new classes of antibody (immunoglobulin, Ig) G and A.

B cells need to do some genetic engineering before they make new classes of antibodies known as Immunoglobulins G or A (IgG or IgA). Image Credit: La Jolla Institute for Immunology

DNA repair proteins

It is estimated by some researchers that chromosomal DNA breaks up to 10,000 times in a single cell in the span of one day. Yet, the consequences of this potentially catastrophic event to the cell are hardly ever felt. The reason is that the body has thousands of proteins dedicated to repairing DNA, to prevent any damage to the DNA.

The moment DNA is damaged by chemical or physical agents, or in the course of the normal wear and tear of daily cellular metabolism, these proteins spring into action to instantly and accurately repair the break without hesitation and without error.

Such DNA repair proteins are ubiquitous in all living species, as indeed they need to be, for without them, life could no longer continue.

HMCES and immune cells

When stimulated by antigens, activated B cells (B lymphocytes) produce various classes of antibodies in the following way. First, they cut out a piece of the double-stranded DNA, that produces IgM antibodies. They then re-join the cut ends (recombine the DNA) in such a way that other forms of antibody are produced, with greater potency. This DNA editing strategy is called class switch recombination (CSR) and scientists have long known that this is used to produce more powerful antibodies.

Prior research has shown that HMCES is a repair protein which fixes nicks or cuts in single strands of DNA. The new study adds a function to its repertoire – alternative end joining, which is what cells in mammals do when the double-strand of DNA is badly severed. In combination with other reports, this shows that HMCES is surprisingly versatile, and carries out multiple tasks to keep the genetic constitution of the organism stable. In the present study, says researcher Vipul Shukla, “We found that HMCES not only recognizes these double strand breaks but helps reseal them.”

How the study began

Some time ago, the laboratory of researcher Anjana Rao at La Jolla Institute for Immunology (LJI) discovered certain regulatory proteins called TET proteins, that could control epigenetic changes by modifying DNA. Such TET-modified proteins could be bound by HMCES. In this way their interest was attracted to HMCES.

To investigate the possibility that HMCES and TET proteins might be similar in the tasks they perform in the body, they produced a knockout of the HMCES gene in experimental mice. From their knowledge of the gene’s role in DNA repair, they thought these mice would probably develop blood cell deficiencies or cancer, since these have been frequently associated with mutations in the TET gene.

However, the results were surprising – these mice had normal blood cells, as well as the expected levels of modified DNA in response to TET.

They then did a comparison between normal B cells and HMCES-deficient B cells with respect to their immune responses. This was based on the plentiful expression of the HMCES protein by normal B cells, which should indicate a key role for this protein in B cell functioning. The researchers found that when the B cells were stimulated by a presented antigen, they switched their antibody class from IgM to IgG. This was much less present in the HMCES-deficient lymphocytes which produced IgG with less efficiency. The reason could be the defect in operation of the CSR processes in the absence of HMCES.

Implications

While this study looked at the role of HMCES in repairing DNA double strands only in lymphocytes, the researchers say this hitherto obscure pathway is active in any body cell, in all probability. Thus, the little-known HMCES protein proves itself to be versatile enough to perform several quite different processes to repair a DNA break.

Earlier research has shown that the type of 3D HMCES structure that binds to a given type of damaged double-stranded DNA determines the task it does. This study confirms that the structure observed here helps the protein to mastermind the alternative end joining activity within B cells. Other studies have shown that sometimes HMCES protects single strands of damaged DNA from being further broken down.

HMCES is unique in being a human protein that shares a single domain with the bacterial protein YedK, known to help repair the DNA of E. coli. This shows that in various organisms, HMCES shows the ability to recognize and respond to different types of DNA damage that require repair to avoid genomic instability.

Mammals and bacteria share the same repair techniques, in short, but HMCES uses this ability to repair introduced and required double-stranded DNA breaks occurring in the course of a normal body process like CSR. Thus, it is part of a broad-based natural repertoire of DNA damage repair proteins that help carry out many vital physiological processes in multiple life forms.