New research shows in detail how a piece of RNA in bacteria — and the ancestor of crucial genetic machinery in humans — cuts itself free from its parent molecule.
This stretch of RNA hops about in the genome of its bacterial hosts, inserting and removing itself as needed. Researchers in RNA scientist Anna Marie Pyle’s lab created detailed molecular maps depicting the conformation of the bacterial RNA and its helper protein at three points as it prepares to begin its travels. Their results were publishedexternal link, opens in a new tab on November 22, 2023.
Over eons of evolution, the descendants of this RNA-protein complex have made their way into other living things. One such RNA machine’s ability to splice genetic material has become indispensable to many organisms, including humans. Because of the long reach of the bacterial system, this work may open a variety of new directions for research.
“These structures have important implications for developing new drugs, for understanding disease and the evolution of these systems,” says Pyle, a Howard Hughes Medical Institute Investigator at Yale University. “And, not least of all, they illustrate the incredibly dynamic behavior of RNA.”
The mother of all splicing machines
This RNA-protein machine, known formally as the group II intron, and its descendants are now found throughout the kingdoms of life. In humans and many other organisms, a member of this lineage, the spliceosome, prepares raw RNA, newly transcribed from DNA, into mRNA, the instructions for making protein. Researchers have looked in detail at the spliceosome, and Pyle’s team wanted to know more about its ancestor, the group II intron.
Scientists already had a basic idea of how the intron system works: It begins as a strand of RNA (black line, below) with a protein, known as maturase (orange), anchoring it in position. That strand loops back on itself, before two successive chemical reactions cut it free from the rest of the RNA.
The first cut occurs when one end (blue) of the strand reacts with a particular component of the RNA’s four-letter code, an adenosine (A), at the base of the loop. The newly freed bit of RNA then contacts the other end (white), cutting the final connection to the intron and connecting the two loose ends of the main strand (blue and white). These steps occur without requiring the cell to burn any of the chemical energy that often powers such reactions.
A team of researchers from Pyle’s laboratory — Ling Xu, a postdoctoral fellow, and Tianshuo Liu and Kevin Chung, both graduate students — decided to take a closer look at the three-dimensional structure of the intron system during this process. With the help from the CryoEM Facilityexternal link, opens in a new tab at HHMI’s Janelia Research Campus, the team used cryo-electron microscopy — in which molecules are frozen then bombarded with electrons — to map the complex at the outset and after each of the two reactions.
From these images, they learned that splicing relies on a mechanical movement by the section of the RNA containing the branchpoint adenosine (red, below). At first anchored to extend horizontally (right), this section swings downward by 90 degrees (left) after the first reaction. This movement sets up the second reaction.
By examining the structures, they identified the source of the energy needed for splicing. A twist in the RNA backbone uncoils after the first reaction, powering the adenosine-containing section’s swing downward.
An ancient system, modern-day meaning
The mechanism uncovered by Pyle’s team appears fundamentally identical to what earlier studies found in its descendant, the spliceosome, according to Max Wilkinsonexternal link, opens in a new tab, an RNA structural biologist and postdoc in HHMI Investigator Feng Zhang’s lab at MIT, who has studied the spliceosome in humans and fungal cells.
While only one protein assists the bacterial RNA, the human and fungal versions require many more, he says. The bacterial system “is accomplishing this in a much simpler way than in us complicated humans.”
This discovery suggests that this mechanism for splicing has likely been around since the early days in the evolution of cells, says Wilkinson, who was not involved in the recent research.
Ancient as the system appears, the team’s findings may have ramifications for modern day health. Because fungal cells possess group II introns, but humans do not, this complex is a potential target for antifungal drugs that selectively disrupt it. Pyle’s group is exploring the intron system as a target to develop drugs against fungal infections including histoplasmosis and its relatives.
Beyond the spliceosome, the group II intron’s likely descendants also include mobile genetic elements, called retrotransposons, that jump about within the human genome. One family of these gene hoppers in human beings, known as LINE-1, has been linked to cancer and autoimmune diseasesexternal link, opens in a new tab.
Group II introns “are good models for learning about not just the spliceosome, but about other similar genetic elements relevant to human health,” Pyle says.
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Citations:
Xu, L., Liu, T., Chung, K. et al. "Structural insights into intron catalysis and dynamics during splicingexternal link, opens in a new tab." 2023. PMID: 37993708
Xiao-Jie, L., Hui-Ying, X., Qi, X. et al. "LINE-1 in cancer: multifaceted functions and potential clinical implicationsexternal link, opens in a new tab." 2016. PMID: 26334179