The inside of a cell is a soup of molecules moving very rapidly; every molecule bumps into every other molecule in its region of the cell countless times every millisecond. Reactions occur. The DNA in the cell nucleus and its attendant handler proteins form a large and complex structure, but this is still a collection of rapidly moving molecules and thus subject to unintended reactions that damage it and break it. Hence there exists a complex collection of proteins in the cell nucleus that act in concert to detect DNA damage and repair DNA. Evolution, by necessity, has made this DNA repair machinery highly efficient. The mutations that we observe in older individuals make up only a tiny, tiny fraction of all of the potentially mutational DNA damage that takes place constantly in every cell in the body.
Mutational DNA damage is thought to be an important contributing factor in degenerative aging, leading to (a) the lethal threat of cancer and (b) somatic mosaicism in tissues, a disruptive influence on the correct function of tissues caused by the slow spread of mutations from stem cell and progenitor cell populations. While it is true that DNA repair machinery is highly efficient in all species, some lower organisms are dramatically more resilient than the average. Typically this was discovered as a result of their response to radiation damage. Some bacteria can survive radiation levels far in excess of the dose needed to kill other species, for example. Is there anything we can learn from these species that might be used to improve DNA repair efficiency in mammals, and thus reduce its contribution to aging?
Today’s open access paper describes the discovery of a compact piece of the DNA repair machinery in a radiation-resistant bacteria that can be transplanted into other bacterial species to dramatically improve their DNA repair. The researchers feel that it should in principle be possible to introduce this protein into higher animals, but have not yet taken that step. Before we get too excited, it is worth noting that putting bacterial proteins, or indeed any foreign protein, into mammals is a project that comes accompanied by many obstacles. The immune system doesn’t like foreign proteins, particularly bacterial, and the established system of regulators and investors is normally strongly opposed to introducing bacterial proteins as a part of therapy – or at least the burden of proof for safety is much higher, and thus development is slower and more expensive, which tends to discourage progress. Still, this is very interesting research, and we can speculate as to how we might best make use of it in human medicine.
Newly discovered protein stops DNA damage
The researchers found the protein – called DdrC (for DNA Damage Repair Protein C) – in a fairly common bacterium called Deinococcus radiodurans (D. radiodurans), which has the decidedly uncommon ability to survive conditions that damage DNA – for example, 5,000 to 10,000 times the radiation that would kill a regular human cell. DdrC scans for breaks along the DNA and when it detects one it snaps shut – like a mousetrap. This trapping action has two key functions: “It neutralizes it (the DNA damage), and prevents the break from getting damaged further. And it acts like a little molecular beacon. It tells the cell ‘Hey, over here. There’s damage. Come fix it.'”
Typically proteins form complicated networks that enable them to carry out a function. DdrC appears to be something of an outlier, in that it performs its function all on its own, without the need for other proteins. The team was curious whether the protein might function as a “plug-in” for other DNA repair systems. They tested this by adding it to a different bacterium: E. coli. “To our huge surprise, it actually made the bacterium over 40 times more resistant to UV radiation damage. This seems to be a rare example where you have one protein and it really is like a standalone machine.”
In theory, this gene could be introduced into any organism – plants, animals, humans – and it should increase the DNA repair efficiency of that organism’s cells. “The ability to rearrange and edit and manipulate DNA in specific ways is the holy grail in biotechnology. What if you had a scanning system such as DdrC which patrolled your cells and neutralized damage when it happened? This might form the basis of a potential cancer vaccine.”
The bacterium Deinococcus radiodurans is known to survive high doses of DNA damaging agents. This resistance is the result of robust antioxidant systems which protect efficient DNA repair mechanisms that are unique to Deinococcus species. The protein DdrC has been identified as an important component of this repair machinery. DdrC is known to bind to DNA in vitro and has been shown to circularize and compact DNA fragments. The mechanism and biological relevance of this activity is poorly understood.
Here, we show that the DdrC homodimer is a lesion-sensing protein that binds to two single-strand (ss) or double-strand (ds) breaks. The immobilization of DNA breaks in pairs consequently leads to the circularization of linear DNA and the compaction of nicked DNA. The degree of compaction is directly proportional with the number of available nicks. Previously, the structure of the DdrC homodimer was solved in an unusual asymmetric conformation. Here, we solve the structure of DdrC under different crystallographic environments and confirm that the asymmetry is an endogenous feature of DdrC. We propose a dynamic structural mechanism where the asymmetry is necessary to trap a pair of lesions. We support this model with mutant disruption and computational modeling experiments.
