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A study gives an idea of ​​DNA damage induced by the sun and cell repair



A study gives an idea of ​​DNA damage induced by the sun and cell repair

The Rad4 / XPC protein interacts dynamically with the DNA duplex to "open" and recognize photoproduct 6-4 (6-4PP), an important DNA lesion induced by sunlight. Here we present a new structure that shows how 6-4PP is completely expelled from the double helix of DNA by the Rad4 / XPC protein that initiates the repair of nucleotide excision. Credit: Nucleic acid research

A team led by a researcher at Baylor University has published a breakthrough article that provides a better understanding of the dynamic process by which the molecular repair machinery of cells recognizes that damage to DNA induced by sunlight needs repair .

Ultraviolet light from the sun is a ubiquitous carcinogen that can cause structural damage to cellular DNA. According to the lead author, Jung-Hyun Min, Ph.D., associate professor of the disease, DNA transports important blueprints for cellular functions, failure to remove and restoration of damaged DNA parts in a timely manner may have results harmful. Chemistry and biochemistry at the Baylor School of Arts and Sciences.

Min and his team demonstrated how the Rad4 / XPC repair protein would bind to one such DNA-induced DNA damage, photoproduct 6-4, to mark the damaged site along the DNA in preparation for the remainder of the process. repair by nucleotide excision (NER) in cells

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

The most important articles present high-impact studies that answer long-standing questions in the field of nucleic acid research and / or open new areas and mechanistic hypotheses for research. They are the best articles published in NAR, which constitute between 1 and 2 percent of those received by the magazine.

UV light threatens the integrity of the genome by causing damage to cellular DNA known as cross-linking damage between chains, Min said. Two main types of these injuries are cycloputane pyrimidine dimer (DPC), which makes up about 70 percent of said hurt; and 6-4 photoproduct (6-4PP), which constitutes approximately 30 percent.

The cellular DNA repair system (NER), which is responsible for eliminating these lesions, works much faster for 6-4PP than for CPD, Min said. This is because a protein that detects DNA damage (called Rad4 / XPC) that initiates NER is more efficient to recognize 6-4PP than to recognize CPD.

Once an injury is limited by Rad4 / XPC, it can be eliminated via the NER pathway. NER works in all organisms, from yeast to humans. According to Min, it is not clear how the Rad4 / XPC protein recognizes lesions and what leads to differences in recognition efficiencies.

The team first determined a 3D structure of the Rad4 protein bound to a DNA substrate containing a 6-4PP lesion, using a technique called X-ray crystallography. The structure showed that the proteins flip out the portions of the DNA it contains. 6-4PP and therefore "open" the double helix of DNA. This was accompanied by a severe unwinding and flexing of the DNA strands.

However, it was not the damaged portion of the DNA that the protein contacted directly, Min said.

Instead, the protein specifically bound to the healthy fragments of the DNA opposite the lesion. This shows that the protein could in principle bind to the CPD, as well as to other DNA lesions induced by the environment that are known to be recognized by Rad4 / XPC. But it could not directly explain why the recognition efficiencies between the injuries may be different.

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

The simulation studies showed that the protein is easily hooked with 6-4PP to unscrew, bend and partially "open" the DNA at the site of the injury. But remarkably, the DNA containing CPD resisted the unscrewing and bending that easily occurred with 6-4PP.

In total, the team was able to assemble a 3-D molecular path that represents the key steps during the "opening" of the DNA performed by Rad4 / XPC and revealed the reasons behind the different recognition of 6-4PP and CPD.

Min believes that the discovery of these repair mechanisms by nucleotide excision could provide benefits beyond understanding UV-induced damage, since NER is also an important pathway that repairs much of the DNA damage induced by the medium environment, including that caused by industrial pollutants, cigarette smoke and even some chemotherapeutic drugs

"The hallmark of NER is that it repairs a very wide range of DNA damage, which is very important in terms of how our genomes are protected from DNA damage caused by the environment," said Min.

"While it has been known for decades that this Rad4 / XPC protein can recognize 6-4PP very efficiently, there has not been a structure that shows how it actually binds to the lesion and why the recognition is so efficient compared to lesions like the CPD., "she said. "Basically, our study fills this missing gap very well and details what that mechanism should be."

While this research showed how Rad4 / XPC can bind to damage in a DNA duplex, it is still unknown how the protein can find such damage if it is in DNA that is organized in a compact manner as it does in cells (called chromatin) .

Min said that most of the DNA in chromatin is wound around proteins called histones and how Rad4 / XPC can move to find an injury is another mystery.

He also said that it is unknown how Rad4 / XPC would recruit the next player from the repair pathway, called Transcription Factor Complex II H (TFIIH), which is important to verify the damage before other proteins arrive and actually eliminate the damaged portion.

"We hope that the knowledge we discover will be useful in solving important problems in human health," said Min. "This is how we imagine we can help, understanding how things work with complete structural details in 3D."


A new mechanism to access damaged DNA.


More information:
Debamite Paul et al. Structure and mechanism of pyrimidine-pyrimidone (6-4) recognition of photoproducts by the repair complex by nucleotide excision Rad4 / XPC, Nucleic acid research (2019). DOI: 10.1093 / nar / gkz359

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A study gives an idea of ​​DNA damage induced by the sun and cell repair (2019, July 14)
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