DNA Invader: Ancient Genetic Colonizer Inhabits Our Genome and Causes Disease-Causing Mutation

As ancient life forms became more complex billions of years ago, a genetic component became a genome colonizer. It replicated and inserted itself again and again into different genomes. As time passed, eukaryotes, including humans, inherited this code. It composed about one-third of the human genome and was considered junk DNA.

This genetic element is LINE-1; its invasion can wreak havoc and cause disease-causing mutations. Its success was enabled by a key protein called ORF2p, whose structure and mechanisms can provide insights into new potential targets for different diseases.

Evolutionary Partners

As a retrotransposon, LINE-1 is a mobile genetic code that translates RNA back into DNA while replicating itself in various places through an organism's genome. Its origin remains mysterious, although it has an evolutionary link to group II introns, a prehistoric mobile element that dates back about 2.5 billion years.

There are various kinds of retrotransposons, such as endogenous retroviruses (ERVs), which resemble Hepatitis B (HBV) and HIV. Retrotransposons like LINE-1 have been undergoing evolution with their host organisms for one to two billion years.

Millions of genetic fragments obtained from LINE-1 are found in our cells. Most of them are inactive evolutionary remains that prove failed attempts to sabotage the replication machinery. About 100 of these elements are operational and usually not helpful.

There has been an ongoing battle between LINE-1 to try to insert itself and the host to protect its genome. The ORF1p protein produced by LINE-1 is churned out by cancer cells, so experts have studied LINE-1 and its proteins for more than a decade. However, ORF2p is expressed very slowly and infrequently, which makes it poorly understood.

LINE-1 has been so difficult to investigate because of its peculiar features. For example, it has an unusual replication cycle and ORF2p protein, which no one has captured.

Understanding LINE-1 Replication

For the first time, scientists from Rockefeller University analyzed the core structure of ORF2p protein in high resolution. In collaboration with over a dozen academic and industry groups, they revealed new insights about the key disease-causing mechanisms of LINE-1.

Led by senior author John LaCava, the researchers used a combination of X-ray crystallography and cryo-EM to purify the full-length ORF2p and a shorter "core" version, which facilitates LINE-1 replication. The team discovered two new folds remaining within ORF2p's core, which contributes to the ability of LINE-1 to make copies of itself.

According to co-first author Trevor van Eeuwen, ORF2p has structural adaptations suited for such endeavors. It is like a jack-of-all-trades protein that can handle everything from replication to insertion. While most viruses need hundreds of reverse transcriptase proteins to replicate, ORF1p does it all.

When LINE-1 gets activated in the cytoplasm, it acts like a viral mimic, which produces RNA: DNA hybrids that look like a viral infection when sensed. This viral mimicry offers a potential solution to activating the innate immune system, contributing to autoimmune disease and other conditions.

In the future, the researchers plan to solve the two newly discovered core domains and seek a better understanding of their functions. For now, they are confident that their research on the structure of ORF2p lays the groundwork for understanding the insertion mechanism of LINE-1.