New machinery digests toxic proteins to protect DNA replication

By Samantha Black, PhD, ScienceBoard editor in chief

March 9, 2020 -- Researchers have identified molecular machinery that helps repair damaged DNA that occurs during DNA replication and transcription. This work, published in Nature Communications on March 9, reveals how specific enzymes "eat" or break down proteins that cause broken DNA.

Topoisomerases are enzymes that participate in the overwinding or underwinding of DNA that arises due to the intertwined nature of the DNA double-helical structure during DNA replication and transcription. Topoisomerase 1 cleavage complexes (TOP1ccs), transient protein complexes that aid the TOP1 enzyme in breaking and rejoining single strands of DNA, can sometimes be cytotoxic by hindering the progression of DNA replication and transcription. This can occur when topoisomerases malfunction or are overexpressed (as is the case in some cancers) and can lead to an accumulation of broken DNA.

Accumulation of damaged DNA can cause cellular damage, cancer, and neurological conditions. Many neurodegenerative diseases are associated with defective TOP1cc repair. Some cancer therapies attempt to stabilize TOP1ccs, but resistance is common. Targeting TOP1cc repair factors could enhance the clinical efficacy of TOP1 poisons and help overcome drug resistance.

"Failure to fix DNA breaks in our genome can impact our ability to enjoy a healthy life at an old age, as well as leave us vulnerable to neurological diseases," said study co-author Sherif El-Khamisy, PhD, professor from the department of molecular biology and biotechnology and the Neuroscience Institute at the University of Sheffield, in a statement. "We hope that by understanding how our cells fix DNA breaks, we can help meet some of these challenges, as well as explore new ways of treating cancer in the future."

In this study, researchers identified gyrase inhibitory-like protein (TEX264) as a cofactor that promotes TOP1cc repair during DNA replication. They specifically found that TEX264 acts with p97 ATPase and spartan (SPRTN) metalloprotein to repair TOP1ccs.

The data shows that the ATPase activity of p97 is required for repair and facilitates the proteolytic digestion of TOP1ccs by SPRTN. P97 and TEX264 enable proteolysis by remodeling the TOP1 protein to make it more amenable to cleavage by SPRTN, which has a catalytic core located within a narrow groove that is only accessible by small, flexible peptides.

Once the bulky protein components of TOP1cc are removed, normal TOP1 can be repaired by tyrosyl-DNA phosphodiesterase 1 (TDP1), allowing for DNA replication to proceed. Together, p97 and TEX264 enable the repair of TOP1ccs by facilitating their proteolysis via SPRTN upstream of TDP1. The researchers show that this process occurs near the nuclear periphery, where TEX264 associates with the DNA replication fork.

The data suggests that the TEX264 machinery preserves genome stability from endogenous TOP1ccs with clinical relevance to TOP1 poisons. To test this theory, the team grew cells that were deficient in TEX264. They found that these cells accumulate endogenous TOP1ccs, exhibit signs of DNA replication stress, and respond to doses of TOP1 poisons. These poisoned cells have an accumulation of broken DNA that may lead to cell death. Therefore, targeting TEX264 to increase the repair of TOP1ccs may offer a new way to treat cancer.

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