Study Provides Insight into Sun-induced Damage to DNA and Cell Repair

A team led by a researcher at Baylor University has published a landmark article that provides insight into the dynamic process by which sunlight-induced DNA damage is recognized by molecular repair machinery in cells. as to be repaired.

The sun's ultraviolet light is an ubiquitous carcinogen that can inflict structural damage to cellular DNA. As DNA has important models for cellular functions, the failure of rapid recovery and restoration of damaged parts of DNA can have adverse consequences and lead to cancers. of the skin in humans, said lead author Jung-Hyun Min, Ph.D., associate professor of chemistry and biochemistry at Baylor College of Arts and Sciences.

Min and his team showed how the Rad4 / XPC repair protein would bind to such UV-induced DNA damage – photoproduct 6-4 – to mark the damaged site along the DNA in preparation of the rest of the nucleotide excision repair (NER) process. in the cells.

The study "Structure and mechanism of the recognition of pyrimidine-pyrimidone photoproducts (6-4) by the Rad4 / XPC nucleotide excision repair complex" – is published in the journal Nucleic acid research (NAR) as a "break article".

The feature articles present high-impact studies addressing long-standing questions in the field of nucleic acid research and / or opening new areas and mechanistic hypotheses for research. These are the best articles published by NAR, representing 1 to 2% of those received by the journal.

UV rays threaten the integrity of the genome by generating damage to cellular DNA, called intra-strand cross-linking damage, Min said. Cyclobutane pyrimidine dimer (CPD) is one of the major types of lesions; it accounts for about 70% of this damage; and 6-4 photoproducts (6-4PP), which is about 30%.

The cellular DNA repair system (NER), responsible for correcting these lesions, works much faster for 6-4PP than CPD, Min said. Indeed, a DNA damage detection protein (called Rad4 / XPC) that initiates TNS is more effective in recognizing 6-4PP than recognizing it.

Once a lesion is linked by Rad4 / XPC, it can be deleted by the NER pathway. NER works in all organisms, from yeast to man. The way the Rad4 / XPC protein recognizes lesions and causes recognition differences in recognition remain unclear, Min said.

The team first determined a 3D structure of the DNA substrate-bound Rad4 protein containing a 6-4PP lesion, using a technique called crystallography The structure has shown that proteins return outward portions of DNA containing 6-4PP and thus "open" the double helix of DNA. This is accompanied by significant decay and flexion of the DNA strands.

However, it is not the damaged part of the DNA that the protein has directly contacted, said Min.

Instead, the protein bound specifically to the healthy DNA fragments opposed to the lesion. This shows that the protein could in principle bind to CPP as well as to other DNA damage induced by the environment and recognized as being recognized by Rad4 / XPC. But that could not explain directly why recognition efficiencies between lesions may be different.

To remedy this, Min then collaborated with Suse Broyde, Ph.D., at the University of New York and used molecular dynamics to computerically simulate the process by which Rad4 can initially hang on. to the DNA containing 6-4PP or CPD.

Simulation studies have shown that the protein easily engages with 6-4PP to untangle, fold and partially "open" the DNA at the site of the lesion. Remarkably, the DNA containing CPD resisted the distortion and bending that easily occurred with 6-4PP.

Overall, the team was able to develop a 3D molecular trajectory that outlines the key steps of DNA opening by Rad4 / XPC and unveiled the reasons for the different recognition of 6-4PP and CPD.

Min believes that the discovery of these mechanisms for nucleotide excision repair could bring benefits beyond understanding UV-induced damage, as NERs are also an important route to repairing many types of damage. to DNA induced by the environment, especially those caused by industrial pollutants, cigarette smoke and even some chemotherapeutic drugs.

"The main feature of NER is that it repairs a very wide range of DNA damage." It's very important for how our genomes are protected from damage to DNA. by the environment, "said Min.

"Although it has been known for decades that this Rad4 / XPC protein can recognize 6-4PP very effectively, there is no structure to show how it actually binds the lesion and why this recognition is so effective. compared to lesions such as CPD, "she says. "Basically, our study nicely fills in this missing gap and details what this mechanism needs to be."

Although this research has shown how Rad4 / XPC can bind to the damage of a DNA duplex, it is still unclear how the protein can detect such damage if it is on compactly organized DNA as in cells (called chromatin).

Min explained that most chromatin DNAs are clustered around proteins called histones and that the way Rad4 / XPC can move to look for a lesion is another mystery.

In addition, she indicated that the means used by Rad4 / XPC to recruit the next actor of the repair pathway, called complex Transcription Factor II H (TFIIH), is important to verify the damage before other proteins do. come and actually cut the damaged part.

"We hope that the knowledge we discover will be useful for solving major human health problems," said Min. "That's how we think we can help – by understanding how things are going with every detail of the 3D structure."