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)

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

Kicking against the PRCs - a domesticated transposase antagonises silencing mediated by polycomb group proteins and is an accessory component of polycomb repressive complex 2

The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity.Fil: Liang, Shih Chieh. University of Edinburgh; Reino UnidoFil: Hartwig, Ben. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Perera, Pumi. University of Edinburgh; Reino UnidoFil: Mora Garcia, Santiago. Fundación Instituto Leloir; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; ArgentinaFil: de Leau, Erica. University of Edinburgh; Reino UnidoFil: Thornton, Harry. University of Edinburgh; Reino UnidoFil: Lima de Alves, Flavia. University of Edinburgh; Reino UnidoFil: Rapsilber, Juri. University of Edinburgh; Reino UnidoFil: Yang, Suxin. University of Edinburgh; Reino UnidoFil: James, Geo Velikkakam. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Schneeberger, Korbinian. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Finnegan, E. Jean. University of Edinburgh; Reino UnidoFil: Turck, Franziska. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Goodrich, Justin. Mc Gill University; Canad

Characterisation of novel regulators of polycombgroup function

Although all cells in a multicellular organism contain the same set of genes, the spatiotemporal expression of these genes needs to be dynamically regulated for morphogenesis and life cycle transitions to take place. Polycomb-group (PcG) proteins are evolutionarily-conserved epigenetic regulators that function – via epigenetic marks such as H3K27me3 and modifications to chromatin structure – to maintain the repression of developmentally-important genes so that these genes are only expressed in the appropriate cells at the appropriate times. This repressive activity of the PcG is antagonised by the trithorax-group (trxG) of proteins. Although they maintain specific patterns of gene repression, PcG proteins are ubiquitously expressed. How their activity is regulated is largely unknown. To identify such regulatory pathways, a genetic screen for modifiers of PcG activity in Arabidopsis was carried out previously using the PcG mutant curly leaf (clf), which has moderately-severe developmental defects due to the ectopic or untimely expression of developmental regulators such as floral homeotic genes and the important flowering time regulator FLOWERING LOCUS T (FT). I characterised three novel potential regulators identified in this genetic screen: the chromatin-associated protein AT-HOOK MOTIF NUCLEAR LOCALISED PROTEIN 22 (AHL22), the 26S proteasome and the novel trithorax-group members ANTAGONIST OF LHP1 1 and 2 (ALP1 and ALP2). I found that the dominant sop-11D mutation is caused by over expression of AHL22 which suppresses the phenotype of clf by reducing FT expression. However, genetic analysis suggests that AHL22 may act in a parallel pathway to the PcG. I showed that mutations affecting diverse subunits of the 26S proteasome reduce the mis-expression of CLF targets and suppress the phenotypes of clf although they do not restore H3K27me3 levels at these targets. Pharmacological inhibition of the proteasome also alleviated the mis-expression of target genes found in clf mutants. Analysis of PcG protein levels following proteasome inhibition suggests that the 26S proteasome antagonises the PcG by degrading the key PcG member EMBRYONIC FLOWER 1 (EMF1), which is likely to be important for implementing target gene repression. Surprisingly, my proteomic analysis showed that the novel trxG members ALP1 and ALP2 are accessory components of a core PcG complex – the Polycomb Repressive Complex 2 (PRC2) – in vivo, suggesting that that ALP1 and ALP2 may antagonise PcG repression by preventing the association of core PRC2 components with accessory components EMF1, LIKE HETEROCHROMATIN PROTEIN 1 and the PHD finger proteins VERNALISATION5 and VIN3-LIKE 1. My results reveal a previously unknown role for 26S proteasomal degradation in the regulation of PcG activity during vegetative development and identify novel in vivo associators of the core PRC2 and point to their role in modulating PcG activity. These results thereby increase our understanding of how the PcG is regulated and serve as a starting point to discover how specificity is given to the PcG mediated repression, either by targeted degradation of EMF1 by various E3 ligases or by different combinations of PRC2 associators

<i>ALP1</i> is widely expressed and its protein product is nuclear-localised.

<p>(A) Complementation assay in <i>clf-50 alp1-4</i> background. The <i>pALP1</i>::<i>ALP1-GFP</i> transgene fully complements <i>alp1-4</i> and restores the clf phenotype, whereas <i>pALP1</i>::<i>ALP1-GUS</i> gives weaker complementation so that plants retain a partially suppressed clf phenotype. (B-G) Histochemical staining showing <i>pALP1</i>::<i>ALP1-GUS</i> activity in rosettes (B), leaves (C), roots (D) and inflorescences (E). (F–G) <i>pALP1</i>::<i>ALP1-GFP</i> is nuclear localised in roots (G), whereas a control <i>35S</i>:<i>GFP</i> construct shows more diffuse localisation in cytoplasm and nucleus (F). Scale bars are 1cm in A, 1mm in B-E and 20μm in F,G.</p

Phylogenetic analysis of ALP1 sequences from land plants and green algae.

<p>Molecular phylogenetic analysis by maximum likelihood (ML) method implemented in MEGA6 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005660#pgen.1005660.ref074" target="_blank">74</a>]. The bootstrap consensus tree inferred from 200 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The composition of the DDE catalytic triad is indicated on the tips of the branches. The tree is unrooted. The species indicated are <i>Arabidopsis thaliana</i>, <i>Glycine max</i> (soybean), <i>Vitis vinifera</i> (grape), <i>Prunus persica</i> (peach), <i>Theobroma cacao</i> (cacao), <i>Ricinus communis</i> (castor bean), <i>Populus trichocarpa</i> (poplar), <i>Solanum lycopersicon</i> (tomato), <i>Oryza sativa</i> (rice), <i>Phoenix dactylifera</i> (date palm), <i>Amborella trichopoda</i>, <i>Cycas micholitzii</i>, <i>Picea sitchensis</i>, <i>Ginkgo biloba</i>, <i>Cyathea spinulosa</i>, <i>Psilotum nudum</i>, <i>Marchantia paleacea</i>, <i>Diphyscium foliosum</i>, <i>Nothoceros vincentianus</i>, <i>Chara braunii</i> and <i>Zea mays</i> (maize). PIF/Harbinger transposase branches are coloured in black, those of green algae in red, bryophytes in blue, pteridophytes in orange, gymnosperms in magenta, the angiosperm ALP1 clade in green, the angiosperm At3g55350 clade in light blue. Genbank accession numbers are prefixed GI, others are accession numbers for sequence retrieved from the 1000 plant genomes website (<a href="http://www.onekp.com" target="_blank">www.onekp.com</a>) with the exception of the <i>Chara braunii</i> sequence which is given the contig number in the transcriptome assembly. The analysis involved 34 amino acid sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous residues were allowed at any position. There were a total of 323 positions in the final dataset.</p

ALP1 interacts with PRC2.

<p>(A) Western blot of seedling protein extracts analysed using anti-CLF antibodies. The left and right panels show blots with short (right panel) and longer (left panel) chemiluminescent detection times as the two extracts from <i>35S</i>::<i>GFP-CLF</i> transgenic plants show much higher expression of GFP-CLF than native CLF. The positions of the size markers in the ladder lane have been marked on the image. Both CLF (≈125kD) and GFP-CLF (≈155 kD) migrate as larger proteins than their predicted sizes (102 and 129 kD, respectively). When the CLF protein was expressed in <i>E</i>. <i>coli</i> it also migrated larger than predicted, possibly because of the high lysine and arginine content in the N-terminal portion. (B-C) Co-immunoprecipitation experiments in which protein extracts were immunoprecipitated using anti-GFP antibodies, immunoblotted and analysed using anti-CLF (B) or anti-MSI1 (C) antibodies. (D-E) Immunoprecipitation of chromatin prepared from 12-day old Ws, <i>clf-5</i>0, <i>alp1-4</i> and <i>clf-50 alp1-4</i> seedlings using anti-H3K27me3 (D) or anti-H3K36me3 (E) antibodies. Precipitated DNA was quantified using real time PCR and is displayed as percentage of input. PCR fragments were located in promoter (pro), transcriptional start site (TSS), exon (ex), intron (in) and at end of interrogated genes as indicated. Error bars indicate the mean and standard error of three separate experiments, each with three technical replicates. The differences between <i>alp1</i> and wild-type or between <i>alp1 clf</i> and <i>clf</i> were not statistically significant (Tukey multiple comparison of means test) in any of the regions examined.</p