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Developmental biology - DNA|
Transposons Control DNA Deletions
Transposons are pieces of DNA that move around within the genome. They are transported by the transposase enzymes they bind to. As they jump around, host organisms can acquire new genes thus gain new functions in a process known as domestication.
A family of transposases called PiggyBac, are repeatedly domesticated by various organisms. How they function is not fully understood, but it is known they play an essential role in Paramecium reproduction.
When single-celled Paramecium divide/reproduce, they undergo huge gene increases followed by a significant drop in gene segment repeats. This excision of gene repeats involves the precise removal of 45,000 non-coding pieces of DNA (called Internal Eliminated Sequences), which would otherwise interrupt 47% of all gene activity in the Paramecium's genome.
In this new work, the team identified five more groups of PiggyBac like transposases (or PgmLs) that work together with PiggyMac (Pgm) to delete specific pieces of DNA in the Paramecium genome. By silencing each different domesticated PiggyBac transposon, researchers found each plays an architectural role and is essential for movement of PiggyMac into the cell nucleus during reproduction where gene domestication/removal occurs.
"We knew that PiggyMac, (Pgm) a domesticated transposase in the PiggyBac family, was responsible for cleaving DNA, but what we didn't know is exactly how the removal machinery is accurately positioned at the ends of this [excised] DNA. The discovery of these new molecules has profound implications for our understanding mechanisms of gene removal (excision) and DNA rearrangement - which plays a crucial role in the development and evolution of many species."
These findings are published in eLife.
Moreover, researchers blocking the activity of PiggyBac transposases caused a number of errors in the gene domestication process. This revealed that although some transposase family members retain their activity level, the process itself becomes less efficient and less accurate over time. It also revealed insights into the preferred lengths for DNA cleaved by these transposase molecules. That some sequences were mechanically difficult to remove shed new light on how there must have been potential constraints on gene deletion in Paramecium during their evolution.
"Our discovery of novel PiggyMac (Pgm) partners, coded by five groups of duplicated genes in the Paramecium genome, brings new insight into the removal mechanism for non-coding sequences by transposases, and a deeper understanding of the machinery involved. Based on our work, future investigations into human domesticated transposases should take into consideration the possibility these molecules may be involved in the same cellular functions."
The domestication of transposable elements has repeatedly occurred during evolution and domesticated transposases have often been implicated in programmed genome rearrangements, as remarkably illustrated in ciliates. In Paramecium, PiggyMac (Pgm), a domesticated PiggyBac transposase, carries out developmentally programmed DNA elimination, including the precise excision of tens of thousands of gene-interrupting germline Internal Eliminated Sequences (IESs). Here, we report the discovery of five groups of distant Pgm-like proteins (PgmLs), all able to interact with Pgm and essential for its nuclear localization and IES excision genome-wide. Unlike Pgm, PgmLs lack a conserved catalytic site, suggesting that they rather have an architectural function within a multi-component excision complex embedding Pgm. PgmL depletion can increase erroneous targeting of residual Pgm-mediated DNA cleavage, indicating that PgmLs contribute to accurately position the complex on IES ends. DNA rearrangements in Paramecium constitute a rare example of a biological process jointly managed by six distinct domesticated transposases.
Julien Bischerour Is a corresponding author , Simran Bhullar, Cyril Denby Wilkes, Vinciane Régnier, Nathalie Mathy, Emeline Dubois, Aditi Singh, Estienne Swart, Olivier Arnaiz, Linda Sperling, Mariusz Nowacki, Mireille Bétermier.
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Acknowledgements This work has benefited from the facilities and expertise of the high throughput sequencing core facility of I2BC (Centre de Recherche de Gif - http://www.i2bc-saclay.fr/). We thank Sylvain Bouvard, Franck Mayeux and Victor Plet for performing preliminary experiments during their master internship, Cindy Mathon and Pascaline Tirand for excellent technical assistance and Arthur Abello, Marc Guérineau, Sandra Duharcourt, Laurent Duret, Eric Meyer, Nelly Morellet, Anne-Marie Tassin and all members of the Duharcourt, Meyer and Tassin laboratories for stimulating discussions. The project was carried out in the framework of the CNRS GDRI ‘Paramecium Genome Dynamics and Evolution’.
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Paramecium with dividing nuclei stained BLUE with DAPI. The large, round nuclei are where
DNA rearrangement takes place. Image credit: Bischerour et al., eLife, 2018.