Uncovering how cells first get their piRNA
Zucchini’s structure (top) is much more similar to an RNA-cutting protein (middle) than to a lipid-cutting one (bottom).
Credit: EMBL/O. Barabas
Click images to enlarge.
In the classic children’s book, Whinnie the Pooh came up against a conundrum every time he had to tell his left paw from his right: “He knew one of them was the right, and he knew that when you had decided which one of them was the right, then the other one was the left. But he never could remember how to begin.” Scientists studying small regulatory RNA molecules called piRNAs have been grappling with a similar issue for decades. Once the cell has some piRNAs, it can use them to produce more – but how is that very first batch produced? Orsolya Barabas’ group at EMBL Heidelberg have now come a step closer to the answer.
Franka Voigt, a PhD student in Orsolya’s lab, determined the 3-dimensional structure of a protein called Zucchini, and, by comparing it to other proteins, was able to solve the mystery of how it acts. Scientists already knew that Zucchini was crucial for producing piRNAs – mice and flies without Zucchini are unable to generate them – but there was an ongoing debate as to why the vegetable-named protein was so important. Most of the proteins in Zucchini’s family act on lipids – the fatty molecules cells use to build membranes – but a few family members cut up DNA and RNA molecules instead. Accordingly, some scientists thought Zucchini might produce the small piRNAs itself, by cutting up longer stretches of RNA, while others suggested that maybe it processed lipids needed to create the niche within the cell where piRNAs are formed.
“When you look at the pictures, it’s pretty obvious even for the uneducated eye that Zucchini is much more like this,” Orsolya says, pointing at the structure of an RNA-cutting protein, “than like that,” pointing at a lipid-cutting family member.
The labs of Mikiko Siomi at Keio University, Japan, and Gregory Hannon and Leemor Joshua-Tor at Cold Spring Harbor, USA, independently reached the same conclusion as Orsolya’s, so this part of the puzzle seems solved: Zucchini is essential for producing piRNAs because it cuts up long RNA strips. But the overall conundrum of piRNA production is by no means untangled. Among other things, scientists now need to work out if Zuchinni cuts the RNA at random points or goes for specific parts, and whether it works alone or with other proteins.
The Barabas group’s study, recently published in RNA, is part of a wider collaboration with Ramesh Pillai’s group at EMBL Grenoble, as both Orsolya and Ramesh are interested in the role of piRNAs and other molecules in controlling what could be a rampant threat to our genomes: transposons, or jumping genes.
Voigt, F., Reuter, M., Kasaruho, A., Schulz, E.C., Pillai, R.S. & Barabas, O. Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc. RNA, published online in advance19 October 2012. DOI: 10.1261/rna.034967.112.