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Scientists Successfully Track Down a “Mystery Gene”

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10/28/2022
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Photo: Peter Haarh/ Netherlands Cancer Institute

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The gene matures the skeleton of the cell.

“I’m a professional pin-in-a-haystack seeker,” geneticist Thijn Brummelkamp responded when asked why he succeeds at finding proteins and genes that others have missed, despite the fact that some have remained elusive for as long as forty years. His research group at the Netherlands Cancer Institute has once again identified one of these “mystery genes” – the gene that guarantees the final form of the protein actin, a key component of our cell skeleton – is produced. These findings were recently published in the journal Science.

Actin is one of the most common molecules in a cell and a key component of the cell skeleton, which is why cell biologists are particularly interested in it. In our lifetime, we produce more than 100 kilograms of actin. It is present in large amounts in all cell types and has a variety of functions, including giving cells structure and making them firmer, playing a key role in cell division, propelling cells forward, and giving our muscles strength. People who have defective actin proteins often have muscle disease. Much is known about actin’s function, but how is the final version of this vital protein produced and which gene is responsible?

“We didn’t know,” says Brummelkamp, whose mission is to find out the function of our genes.

Genetics in haploid human cells

Brummelkamp has developed a number of unique methods for this purpose over the course of his career, which allowed him to be the first to inactivate genes on a large scale for his genetics research in human cells twenty years ago. “You can’t crossbreed people like fruit flies, and see what happens.” Since 2009, Brummelkamp and his team have been using haploid cells – cells containing only one copy of each gene instead of two (one from your father and one from your mother). While this combination of two genes forms the basis of our entire existence, it also creates unwanted noise when conducting a genetics experiment because mutations usually occur in just one version of a gene (the one from your father, for example) and not the other.

Multi-purpose method for genetics in human cells

Together with other researchers, Brummelkamp uses this multi-purpose method to find the genetic causes of particular conditions. He has already shown how the Ebola virus and a number of other viruses, as well as certain forms of chemotherapy, manage to enter a cell. He also investigated why cancer cells are resistant to certain types of therapy and discovered a protein found in cancer cells that acts as a brake on the immune system. This time he went looking for a gene that matures actin – and as a result, the skeleton of the cell.

In search of scissors

Before a protein is completely “finished” – or mature, as the researchers describe it in Science – and can fully perform its function in the cell, it usually has to be stripped of a specific amino acid

Any substance that when dissolved in water, gives a pH less than 7.0, or donates a hydrogen ion.

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Peter Haahr, a postdoc in Brummelkamp’s group, worked on the following experiment: first, he caused random mutations (mistakes) in random haploid cells. Then he selected the cells containing the immature actin by adding a fluorescently labeled antibody to his cells that fit in the exact spot where the amino acid is cut off. As a third and final step, he investigated which gene mutated after this process.

They called it ‘ACTMAP’

Then came the “eureka”-moment: Haahr had traced down the molecular scissors that cut the essential amino acid from actin. Those scissors turned out to be controlled by a gene with a previously unknown function; one no researcher had ever worked with. This means that the researchers were able to name the gene themselves, and they settled on ACTMAP (ACTin MAturation Protease).

To test whether a lack of ACTMAP leads to issues in living things, they switched off the gene in mice. They observed that the actin in the cell skeleton of these mice remained unfinished, as expected. They were surprised to find that the mice did stay alive, but suffered from muscle weakness. The researchers conducted this research together with scientists from VU Amsterdam.

More scissors found in the skeleton of the cell

ACTMAP is not the first mystery gene discovered by Brummelkamp that plays a role in our cell skeleton function. Using the same method, his group has been able to detect three unknown molecular scissors over recent years that cut an amino acid from tubulin, the other main component of the cell skeleton. These scissors allow tubulin to perform its dynamic functions properly inside the cell. The last scissors (MATCAP) were discovered and described in Science this year. Through this earlier work on the cell skeleton, Brummelkamp managed to arrive at actin.

Mission: mapping out all 23.000 genes

“Unfortunately, our new discovery about actin doesn’t tell us how to cure certain muscular conditions,” says Thijn Brummelkamp. “But we have provided new fundamental knowledge about the cell skeleton that may be useful to others later.” Moreover, Brummelkamp, whose mission is to be able to map out the function of all of our 23,000 genes one day, can tick another new gene off his gigantic list. After all, we don’t know what half of our genes do, which means that we cannot intervene when something goes wrong.

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Schedule8 Feb 2023