The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)

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 plantspecific accessory components such as the H3K27me3 reader LIKE HETEROCHROMA-TION 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

A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

“…Harbinger transposon-derived proteins co-purify with HDA6 and MBD proteins HDP1 and ALP1 are Harbinger transposase-derived proteins and function as components of two distinct chromatin modifying complexes (Liang et al, 2015;Duan et al, 2017;Velanis et al, 2020). Since HHP1 is also a Harbinger transposon-derived protein (Liang et al, 2015), we next undertook a proteomics approach to test whether HHP1, like ALP1 and HDP1, is part of a chromatin modifying complex.…”

“…In both published examples of domesticated Harbinger transposases in Arabidopsis, the nuclease-derived component (HDP1 or ALP1) retained its cooperation with the protein derived from the DNA-binding domain (HDP2 or ALP2) (Duan et al, 2017;Velanis et al, 2020). The ancestral Harbinger DNA-binding component shows limited similarity to SANT/ Myb/trihelix motif proteins (Kapitonov and Jurka, 2004;Duan et al, 2017).…”

“…Interaction between these two proteins is required to reconstitute transposase activity and effective transposition of PIF/Harbinger elements (Sinzelle et al, 2008;Hancock et al, 2010). Several genes that originated by domestication of PIF/Harbinger transposases have been reported to play critical roles in regulating gene expression (Liang et al, 2015;Duan et al, 2017;Velanis et al, 2020). For instance, Arabidopsis HARBINGER DE-RIVED PROTEIN 1 (HDP1) and HDP2, a pair of anti-silencing factors derived from Harbinger transposons, can interact with one another and also associate with INCREASED DNA METHYLATION 1 (IDM1), IDM2, IDM3 as well as METHYL-CPG-BINDING DOMAIN 7 (MBD7) to form a histone acetyltransferase complex that prevents hypermethylation and silencing of specific loci (Duan et al, 2017).…”

“…For instance, Arabidopsis HARBINGER DE-RIVED PROTEIN 1 (HDP1) and HDP2, a pair of anti-silencing factors derived from Harbinger transposons, can interact with one another and also associate with INCREASED DNA METHYLATION 1 (IDM1), IDM2, IDM3 as well as METHYL-CPG-BINDING DOMAIN 7 (MBD7) to form a histone acetyltransferase complex that prevents hypermethylation and silencing of specific loci (Duan et al, 2017). ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) and ALP2 are another pair of domesticated Harbinger-derived proteins that antagonize silencing mediated by Polycomb group (PcG) proteins (Liang et al, 2015;Velanis et al, 2020). ALP1 and ALP2 associate with MSI1, a core component of the H3K27me3 histone methyltransferase complex Polycomb repressive complex 2 (PRC2), and may displace the accessory components EMBRYONIC FLOWER 1 (EMF1) and LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) to form a variant PRC2 complex (Velanis et al, 2020).…”

“…ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) and ALP2 are another pair of domesticated Harbinger-derived proteins that antagonize silencing mediated by Polycomb group (PcG) proteins (Liang et al, 2015;Velanis et al, 2020). ALP1 and ALP2 associate with MSI1, a core component of the H3K27me3 histone methyltransferase complex Polycomb repressive complex 2 (PRC2), and may displace the accessory components EMBRYONIC FLOWER 1 (EMF1) and LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) to form a variant PRC2 complex (Velanis et al, 2020). Phylogenetic analysis indicates that there are at least four other domesticated Harbinger-related nucleases in Arabidopsis (Duan et al, 2017).…”