Evolution of SET-Domain Protein Families in the Unicellular and Multicellular Ascomycota Fungi

Background: The evolution of multicellularity is accompanied by the occurrence of differentiated tissues, of organismal developmental programs, and of mechanisms keeping the balance between proliferation and differentiation. Initially, the SET-domain proteins were associated exclusively with regulation of developmental genes in metazoa. However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. However, comparisons across the unicellular and multicellular domains of life are complicated by the lack of knowledge of the ancestral SET-domain genes. Even within the crown group, different biological systems might use the epigenetic \u27code\u27 differently, adapting it to organism-specific needs. Simplifying the model, we undertook a systematic phylogenetic analysis of one monophyletic fungal group (Ascomycetes) containing unicellular yeasts, Saccharomycotina (hemiascomycetes), and a filamentous fungal group, Pezizomycotina (euascomycetes). Results: Systematic analysis of the SET-domain genes across an entire eukaryotic phylum has outlined clear distinctions in the SET-domain gene collections in the unicellular and in the multicellular (filamentous) relatives; diversification of SET-domain gene families has increased further with the expansion and elaboration of multicellularity in animal and plant systems. We found several ascomycota-specific SET-domain gene groups; each was unique to either Saccharomycotina or Pezizomycotina fungi. Our analysis revealed that the numbers and types of SET-domain genes in the Saccharomycotina did not reflect the habitats, pathogenicity, mechanisms of sexuality, or the ability to undergo morphogenic transformations. However, novel genes have appeared for functions associated with the transition to multicellularity. Descendents of most of the SET-domain gene families found in the filamentous fungi could be traced in the genomes of extant animals and plants, albeit as more complex structural forms. Conclusion: SET-domain genes found in the filamentous species but absent from the unicellular sister group reflect two alternative evolutionary events: deletion from the yeast genomes or appearance of novel structures in filamentous fungal groups. There were no Ascomycota-specific SET-domain gene families (i.e., absent from animal and plant genomes); however, plants and animals share SET-domain gene subfamilies that do not exist in the fungi. Phylogenetic and genestructure analyses defined several animal and plant SET-domain genes as sister groups while those of fungal origin were basal to them. Plants and animals also share SET-domain subfamilies that do not exist in fungi

The UBC9 E2 SUMO conjugating enzyme binds the PR-Set7 histone methyltransferase to facilitate target gene repression.

PR-Set7/Set8/KMT5a is a chromatin-modifying enzyme that specifically monomethylates lysine 20 of histone H4 (H4K20me1). In this study we attempted to identify PR-Set7-interacting proteins reasoning that these proteins would provide important insights into the role of PR-Set7 in transcriptional regulation. Using an unbiased yeast two-hybrid approach, we discovered that PR-Set7 interacts with the UBC9 E2 SUMO conjugating enzyme. This interaction was confirmed in human cells and we demonstrated that PR-Set7 was preferentially modified with SUMO1 in vivo. Further in vitro studies revealed that UBC9 directly binds PR-Set7 proximal to the catalytic SET domain. Two putative SUMO consensus sites were identified in this region and both were capable of being SUMOylated in vitro. The absence of either or both SUMO sites did not perturb nuclear localization of PR-Set7. By employing whole genome expression arrays, we identified a panel of genes whose expression was significantly altered in the absence of PR-Set7. The vast majority of these genes displayed increased expression strongly suggesting that PR-Set7 predominantly functions as a transcriptional repressor. Importantly, the reduction of UBC9 resulted in the consistent derepression of several of these newly identified genes regulated by PR-Set7. Our findings indicate that direct interaction with UBC9 facilitates the repressive effects of PR-Set7 at specific target genes, most likely by SUMOylating PR-Set7

PR-Set7 is selectively modified by SUMO1 in cells and SUMOylated at K110 or K131 <i>in vitro</i>.

<p>(A) HEK 293 cells were co-transfected with the indicated expression plasmids. Cell extracts were prepared in the presence of NEM 2 days post-transfection, followed by immunoprecipitations using an anti-HA antibody. HA-bound samples were fractionated by SDS-PAGE prior to Western analysis using anti-FLAG or anti-HA antibodies. (B) Two putative PR-Set7 SUMOylation sites, one perfect and one partial, were identified using SUMOsp 2.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022785#pone.0022785-Ren1" target="_blank">[40]</a>. ClustalX was used to align the sequence surrounding the putative SUMO sites of PR-Set7 in various organisms. Conserved residues are shaded and red asterisks mark K110 and K131. (C) Recombinant wild type PR-Set7, N-terminal (aa1–191) or C-terminal (aa192–352) fragments were used as substrates in <i>in vitro</i> SUMOylation assays. Reactions were fractionated by SDS-PAGE gel followed by Western analysis using anti-His and anti-SUMO1 antibodies. Asterisk (*) denotes an unknown contaminating protein. (D) Recombinant wild type PR-Set7, K110R, K131R or K110/131R double mutant were used as substrates in <i>in vitro</i> SUMOylation assays. Reactions were fractionated by SDS-PAGE followed by Western analysis using anti-PR-Set7 antibodies.</p

Genes whose expression change >2-fold in cells lacking PR-Set7.

<p>Genes whose expression change >2-fold in cells lacking PR-Set7.</p

The K110 and K131 SUMOylation sites are dispensable for nuclear localization of PR-Set7.

<p>HEK 293 cells transfected with GFP-PR-Set7 wild type, K110R, K131R or K110R/K131R mutants (green) were fixed, stained with DAPI (blue) and visualized using a Zeiss Axio Imager upright fluorescence microscope.</p

UBC9 directly binds the N-terminal region of PR-Set7.

<p>(A) The indicated recombinant fusion proteins were expressed in <i>E. coli</i>, purified by affinity chromatography and fractionated by SDS-PAGE. (B) Purified recombinant S-tag-PR-Set7 was incubated with GST-UBC9 or GST alone prior to an S-tag immunoprecipitation. Western analysis of the bound material was performed using UBC9 and His antibodies. (C) ³⁵S-labeled PR-Set7 was incubated with GST-UBC9 or GST alone prior to GST pull downs. PR-Set7 binding was determined by autoradiography. Western analysis of the input (In) and bound (B) fractions were performed using GST antibodies to confirm equal loading. (D) Purified recombinant His-tagged N- and C-terminal PR-Set7 proteins were incubated with GST-UBC9 or GST alone prior to GST pull downs. Western analysis of the bound fractions was performed using His and GST antibodies.</p

UBC9 transiently interacts with PR-Set7 in cells.

<p>(A) HEK 293 cell lysates expressing FLAG-PR-Set7 or FLAG-null were immunoprecipitated with an UBC9 antibody. Western analysis of the input (In) and bound (B) fractions were analyzed using FLAG or UBC9 antibodies. (B) HEK 293 cells co-transfected with the indicated plasmids were crosslinked using 10 µM BMH prior to FLAG-immunoprecipitations. Western analysis was performed using Myc or FLAG antibodies on the input (In), unbound (U) and bound (B) fractions.</p

Yeast two-hybrid screen identifies UBC9 as a PR-Set7-interacting protein.

<p>(A) Schematic representation of the different Gal4-DBD-PR-Set7 bait proteins used for the yeast two-hybrid screen and the recovered AD-UBC9. (B) The indicated plasmids were co-transformed into AH109 yeast strain and grown on medium lacking: tryptophan and leucine (DDO), and histidine (TDO) and adenine with addition of X-alpha-galactosidase (QDO). Growth on TDO and QDO indicates interaction between PR-Set7 and UBC9. (C) Western analysis of HA-immunoprecipitations from yeast co-transformants expressing the indicated plasmids using PR-Set7 and UBC9 antibodies on the input (In), unbound (U) and bound (B) fractions.</p