Dimerization of a viral SET protein endows its function

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 10/2010; 107(43):18433-8. DOI: 10.1073/pnas.1009911107
Source: PubMed


Histone modifications are regarded as the most indispensible phenomena in epigenetics. Of these modifications, lysine methylation is of the greatest complexity and importance as site- and state-specific lysine methylation exerts a plethora of effects on chromatin structure and gene transcription. Notably, paramecium bursaria chlorella viruses encode a conserved SET domain methyltransferase, termed vSET, that functions to suppress host transcription by methylating histone H3 at lysine 27 (H3K27), a mark for eukaryotic gene silencing. Unlike mammalian lysine methyltransferases (KMTs), vSET functions only as a dimer, but the underlying mechanism has remained elusive. In this study, we demonstrate that dimeric vSET operates with negative cooperativity between the two active sites and engages in H3K27 methylation one site at a time. New atomic structures of vSET in the free form and a ternary complex with S-adenosyl homocysteine and a histone H3 peptide and biochemical analyses reveal the molecular origin for the negative cooperativity and explain the substrate specificity of H3K27 methyltransferases. Our study suggests a "walking" mechanism, by which vSET acts all by itself to globally methylate host H3K27, which is accomplished by the mammalian EZH2 KMT only in the context of the Polycomb repressive complex.

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Available from: Ming-Ming Zhou, May 01, 2014
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    • "A conserved SET domain methyltransferase from Paramecium bursaria chlorella viruses, termed vSET, uses a ‘walking’ mechanism to suppress host transcription by methylating histone H3 at lysine 27 (H3K27), a mark for eukaryotic gene silencing induction [22]. vSET is the smallest methyltransferase and functions as a dimer [22], in a sharp contrast to the H3K27 methyltransferase EZH2, which is monomeric and relies on polycomb repressive complex 2 (PRC2) partners to achieve optimal activity [44]. When fused to the GAL4 DNA-binding domain, it effectively inhibits the target promoter in 293 T cells [23]. "
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    ABSTRACT: Background Targeted gene silencing is an important approach in both drug development and basic research. However, the selection of a potent suppressor has become a significant hurdle to implementing maximal gene inhibition for this approach. We attempted to construct a ‘super suppressor’ by combining the activities of two suppressors that function through distinct epigenetic mechanisms. Results Gene targeting vectors were constructed by fusing a GAL4 DNA-binding domain with a epigenetic suppressor, including CpG DNA methylase Sss1, histone H3 lysine 27 methylase vSET domain, and Kruppel-associated suppression box (KRAB). We found that both Sss1 and KRAB suppressors significantly inhibited the expression of luciferase and copGFP reporter genes. However, the histone H3 lysine 27 methylase vSET did not show significant suppression in this system. Constructs containing both Sss1 and KRAB showed better inhibition than either one alone. In addition, we show that KRAB suppressed gene expression by altering the histone code, but not DNA methylation in the gene promoter. Sss1, on the other hand, not only induced de novo DNA methylation and recruited Heterochromatin Protein 1 (HP1a), but also increased H3K27 and H3K9 methylation in the promoter. Conclusions Epigenetic studies can provide useful data for the selection of suppressors in constructing therapeutic vectors for targeted gene silencing.
    Full-text · Article · Aug 2014 · Epigenetics & Chromatin
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    • "Since the initial sequencing of the prototype CV, Paramecium bursaria chlorella virus 1 [13,14], more than 15 years ago, only 5 more whole-genome sequences of CVs have been reported [15-17]. These 6 sequences reveal many features that distinguish them from other NCLDV including genes encoding a translation elongation factor EF-3, enzymes required to glycosylate proteins [18], enzymes required to synthesize the polysaccharides hyaluronan and chitin, polyamine biosynthetic enzymes, proteins that are ion transporters and ones that form ion channels including a virus-encoded K+ channel (designated Kcv) [19], a SET domain-containing protein (referred to as vSET) that dimethylates Lys27 in histone 3 [20,21], and many DNA methyltransferases and DNA site-specific endonucleases [22,23]. Moreover, the evolution of large DNA viruses is subject to intense debate. "
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    ABSTRACT: Background Giant viruses in the genus Chlorovirus (family Phycodnaviridae) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses in public databases. Presented here are the draft genome sequences of 35 additional chloroviruses (287 – 348 Kb/319 – 381 predicted protein encoding genes) collected across the globe; they infect one of three different green algal species. These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses. Results Genome colinearity, nucleotide conservation and phylogenetic affinity were limited to chloroviruses infecting the same host, confirming the validity of the three previously known subgenera. Clues for the existence of a fourth new subgenus indicate that the boundaries of chlorovirus diversity are not completely determined. Comparison of the chlorovirus phylogeny with that of the algal hosts indicates that chloroviruses have changed hosts in their evolutionary history. Reconstruction of the ancestral genome suggests that the last common chlorovirus ancestor had a slightly more diverse protein repertoire than modern chloroviruses. However, more than half of the defined chlorovirus gene families have a potential recent origin (after Chlorovirus divergence), among which a portion shows compositional evidence for horizontal gene transfer. Only a few of the putative acquired proteins had close homologs in databases raising the question of the true donor organism(s). Phylogenomic analysis identified only seven proteins whose genes were potentially exchanged between the algal host and the chloroviruses. Conclusion The present evaluation of the genomic evolution pattern suggests that chloroviruses differ from that described in the related Poxviridae and Mimiviridae. Our study shows that the fixation of algal host genes has been anecdotal in the evolutionary history of chloroviruses. We finally discuss the incongruence between compositional evidence of horizontal gene transfer and lack of close relative sequences in the databases, which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.
    Full-text · Article · Mar 2013 · BMC Genomics
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    ABSTRACT: The recent identification of giant viruses has raised important questions, not only regarding their origin and evolution, but also regarding the differentiation between viruses and living organisms. These viruses possess large genomes encoding genes potentially involved in various metabolic processes and even protein synthesis, indicating their putative autonomy. Giant viruses of the Phycodnaviridae and Mimiviridae families appear to share a common evolutionary ancestor with members of the nucleo-cytoplasmic large DNA viruses. Many giant viruses are associated with protists in aquatic environments and might have evolved in protist cells. They may therefore play important roles in material cycling in natural ecosystems. With the advent of environmental metagenomic projects, there will be more chances to encounter novel giant viruses in the future.
    Full-text · Article · Jul 2011
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