Shedding light on the mechanism of DNA repair in yeast

DNA damage is a cellular phenomenon that results in structural abnormalities in double-stranded DNA. External factors such as radiation or chemical substances as well as internal factors such as blocked DNA replication can cause double-strand breaks (DSBs) in DNA.

To counteract DNA damage, cells perform DNA repair to preserve genetic integrity and ensure cell survival, because failed repair of DNA blocks can lead to serious health complications, such as an increased risk of cancer.

Repair of DNA double-strand breaks occurs through two mechanisms called non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the predominant DNA repair mechanism in human body cells and is error-prone. In contrast, HR is active and error-free during certain phases of the cell cycle.

The trimeric protein complex Mre11-Rad50-Xrs2 (MRX) in yeast plays a central role in HR. Sae2, a cellular protein, coordinates with MRX to stimulate endonuclease and exonuclease activities to initiate DNA end resection. DNA end resection is a two-step process for DNA end-knot repair.

In short-distance resection, the MRX-Sae2 endonuclease makes a cut in the 5′ strand. It then activates the 3′-5′ exonuclease to digest a few base pairs of the 5′ strand, creating stretches of single-stranded DNA. In long-distance resection, the Exo1 exonuclease extends the resection in the 5′-3′ direction and helps with DNA repair.

In a study published in Nature communication On August 22, 2024, an international research team attempted to understand the controlled mechanism and physiological significance of Sae2 in DNA repair.

The team, consisting of Professor Miki Shinohara and Mr Tomoki Tamai from Kindai University, Japan, Dr Giordano Reginato and Dr Petr Cejka from Università della Svizzera italiana, Switzerland, and Dr Katsunori Sugimoto from the State University of New Jersey, USA, performed genetic and biochemical analyses to investigate how Sae2 controls the two nuclease activities.

Prof. Shinohara explains: “The mechanism by which Sae2 stimulates MRX endonuclease and 3′-5′ exonuclease activities for DNA repair is still unknown. Understanding this mechanism of DNA end processing in DNA double-strand break repair can expand our knowledge of the plasticity and robustness of genetic information in organisms.”

In a separation of function experiment, the researchers identified and introduced the mutation Rad50-C47, which affects the Sae2-dependent MRX 3′-5′ exonuclease activity but not the endonuclease activity.

“Our results suggest that MRX endo- and exonuclease activities are stimulated by Sae2 via Rad50 through different mechanisms, ensuring coordinated but separate endonucleolytic and exonucleolytic effects of MRX-Sae2 on blocked DNA ends,” says Prof. Shinohara.

To maintain the robustness of the process that preserves genetic information in organisms, it is crucial to understand exactly how Sae2 regulates the endo- and exonuclease activities of Mre11 during DNA end resection in DNA double-strand break repair.

“Our study reveals the control mechanism for DNA end processing, which is important for suppressing cell tumorigenesis and could provide valuable information for the development of new cancer therapies,” concludes Prof. Shinohara.