Abstract
A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes.
Highlights
A large fraction of plant and animal genomes is made up of transposable elements (TE), and even in plant species such as Arabidopsis thaliana, which has a relatively small genome, 15% of the genome is comprised of TE [1]
A large part of the genomes of plants and animals consists of transposable elements (TE), which are usually considered as selfish or parasitic as they encode proteins which promote TE proliferation but not functions useful for their hosts
We have identified the ALP proteins, two domesticated transposases which function as components of an enzyme complex (PRC2) involved in modifying chromatin and regulating host gene activity in plants
Summary
A large fraction of plant and animal genomes is made up of transposable elements (TE), and even in plant species such as Arabidopsis thaliana, which has a relatively small genome, 15% of the genome is comprised of TE [1]. Hosts have consistently evolved surveillance mechanisms that monitor and inhibit TE activity These involve hosts producing small RNA molecules with homology to TE transcripts, leading to the local recruitment of repressive epigenetic machinery to TE chromatin and to the silencing of the genes encoding the transposase proteins that catalyse transposition and proliferation [for reviews see 2, 3]. Domesticated transposases have been identified both from forward genetic screens based on phenotypes, but increasingly from bioinformatic analysis of genome sequences; in the latter, identification is based on a suite of common properties including sequence similarity with functional transposases, low copy number, a conserved genomic location in different species (immobilisation), detectable expression, and a lack of TE-associated features such as terminal inverted repeats [for review see 9] These features allowed identification of 36 novel genes putatively derived from domesticated transposases in Arabidopsis, and there are likely many more that escaped detection because their sequences have diverged sufficiently that similarities to transposases are no longer apparent [10]. Similar approaches have identified domesticated transposases in vertebrates and flies [11, 12] but in most cases the function of these genes is unknown, raising the question as to whether each has acquired a different role or whether there are common functions
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