Make Peace not War

“The best way to destroy an enemy is to make him a friend”. Abraham Lincoln’s political wisdom can also be transferred to evolution as illustrated by many examples of mutually beneficial interactions or even symbioses between species that started out as deadly adversaries.

Researchers from the Max Planck Institute for Plant Breeding Research in Cologne together with scientists from the University of Edinburgh in Scotland show how this applies even to transposable elements sometimes also referred to as “jumping genes”. The groups show how one of these was distracted from its original intent to invade the plant host genome to become part of a regulatory pathway regulating genes with key functions in plant development.

Despite differences in their body plan and developmental strategy, both, plants and animals are dependent on cellular memories, which are mediated by so-called epigenetic regulation of key developmental genes. Epigenetic mechanisms of gene regulation make use of chromatin, the DNA packaging structure in the nucleus, by placing genes in either an accessible chromatin state or locking them away for good in particularly compacted chromatin. Such archiving of genes in inaccessible chromatin is also a common strategy to keep invasive transposable elements in check as these are dependent on their transcription to multiply.

Justin Goodrich from the University of Edinburgh, Franziska Turck at the MPIPZ and their collaborators share the interest in epigenetic regulation of plant development. Both groups initiated genetic screens in the genetic model plant Arabidopsis thaliana to identify genes that are able to alleviate the effect of mutations in the Polycomb Group (PcG) pathway, which is the major pathway for epigenetic repression of developmental genes. Although they searched for genetic suppressors of different primary PcG mutants, they discovered that mutation of the same gene, now named ANTAGONIST OF LHP1 (ALP1) substantially suppressed the phenotype of the primary mutants. In the spirit of Lincoln’s stratagem, the groups decided to collaborate rather than compete in the further characterization of their respective mutants. Fortuitously, a call for collaborative projects within the European Union, the ERA-PG Plant Genomics, had just been launched providing the groups with the necessary means to pursue their work.

Their first assumption was that ALP1 was a constituent of protein complexes capable of moving target genes from their chromatin archive to a more accessible state. Such genes, collectively termed the Trithorax Group (TrxG), were first described in fruit flies where they had been identified by similar genetic screens for suppressors of mutations in the PcG pathway. In general, proteins and protein complexes of the TrxG participate in the process of transcription and leave small “tags” in the form of chemical modifications at proteins that are part of the chromatin structure. Presence of these tags inhibits the action of PcG complexes. Indeed a large number of genes that were misregulated in the original PcG mutants showed a much more wild-type like expression in combination with the mutation in ALP1. However, developmental phenotypes caused by adding mutations in ALP1 to those of known TrxG genes were additive, a first indication that the mechanism was going to be different.

Making use of the proteomics expertise in Juri Rappsilber’s unit at the University of Edinburgh, the collaborators were able to identify proteins that formed complexes with ALP1. Surprisingly, a subpopulation of PcG proteins, called Polycomb Repressive Complex 2 (PRC2) was predominantly enriched in co-purifications. This indicated that ALP1 could act as a direct repressor of PRC2 catalytic activity, which is the modification of a lysine residue of the amino-terminal tail of histone H3, a component of chromatin. An alternative hypothesis was suggested by the reciprocal purification experiment, which identified proteins associated with the PRC2 component CURLY LEAF (CLF). CLF co-purified with other PRC2 components and ALP1 as expected, but also with additional components previously attributed to a distinct PcG complex, named PRC1. Epigenetic repression of genes requires the concerted action of both PRC2 and PRC1 and therefore ALP1 may function by sequestering a pool of PRC2 that cannot at the same time interact with PRC1 components. Liberating that pool in the alp1 mutant would allow recovery of defects in PcG mediated gene repression. Notably, the mutation in ALP1 suppresses so called weak PcG mutants that are only partially compromised but not strong mutants largely defective in the pathway.

“It could be that the original transposase tried to fight the repressive chromatin complexes and that this function became integrated to the regulation of the pathway” speculates Justin Goodrich. Phylogenetic analysis suggests that the domestication of ALP1 occurred at the root of angiosperm diversification at which point a mutation in an amino-acid motif important for endolytic cleavage of DNA was fixed, likely rendering the protein catalytically inactive. This point in evolution is marked by key innovations such as the formation of ovaries developing into fruits and of true flowers with a veritable explosion in diversity of form and shape. “Transposable elements are repressed by PcG complexes in the endosperm early in seed development while in adult plants other pathways take over this function. ALP1’s conversion from foe to friend could be connected to this tissue, which is unique to angiosperms” says Franziska Turck.

Interestingly, ALP1’s ancestor belonged to the Harbinger transposases of which one member, named Harbinger Transposase Derived 1 (Harbi1) became also domesticated in vertebrates. This could be coincidence but also indicate that an interaction of Harbinger transposases with chromatin made them good candidates for domestication. As every novel result, the discovery of ALP1 as accessory to PRC2 raises many new questions giving the groups ample opportunity to pursue their fruitful collaboration to provide answers to some of them.