How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or ‘emergent’ sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers. These binding sites were biochemically validated by EMSA-FRET analysis and validated in vivo by ChIP-seq data from human cell lines. Focusing on ATF3, we observed distinct cognate site preferences conferred by different bZIP partners, and demonstrated that genome-wide binding of ATF3 is best explained by considering many dimers in which it participates. Importantly, our compendium of bZIP-DNA interactomes predicted bZIP binding to 156 disease associated SNPs, of which only 20 were previously annotated with known bZIP motifs.

Microsporidian diversity is vast. There is a renewed drive to understand how microsporidian pathological, genomic, and ecological traits relate to their phylogeny. We comprehensively sample and phylogenetically analyse 125 microsporidian genera for which sequence data are available. Comparing these results with existing phylogenomic analyses, we suggest an updated taxonomic framework to replace the inconsistent clade numbering system, using informal taxonomic names: Glugeida (previously clades 5/3), Nosematida (4a), Enterocytozoonida (4b), Amblyosporida (3/5), Neopereziida (1), and Ovavesiculida (2). Cellular, parasitological, and ecological traits for 281 well-defined species are compared with identify clade-specific patterns across long-branch Microsporidia. We suggest that future taxonomic circumscriptions of Microsporidia should involve additional markers (SSU/ITS/LSU), and that a comprehensive suite of phenotypic and ecological traits help to predict broad microsporidian functional and lineage diversity.

Overview Microsporidia are obligate intracellular parasites that can infect a wide range of hosts. They cause death and disease in both humans and agriculturally important animals. They have also become a powerful model for understanding the evolution of intracellular parasites. Recent work has explored how microsporidia genomes have evolved, the evolutionary origins of microsporidia, and how microsporidia adapt to interact with their hosts. What do microsporidia have in common? Microsporidia can only exist outside of their host as environmentally resistant, chitin-containing spores. These spores contain a unique infectious apparatus known as the polar tube. During infection, the polar tube is rapidly discharged and can pierce a host cell, depositing the parasite's sporoplasm within the host cell [1]. The sporoplasm then proliferates, eventually producing spores that then exit the host to cause subsequent infections. Microsporidia are thought to reproduce mostly asexually, although most are likely diploid based on genomic heterozygosity and conservation of meiotic genes [2-5]. Because of the intimate relationship between microsporidia and their hosts, they are heavily dependent on host resources and have undergone extensive genomic reduction [6,7]. Analysis of sequenced microsporidia genomes (Fig 1A) has revealed a wide loss of protein families that are present in other eukaryotes, leaving only approximately 800 conserved microsporidia proteins [6]. The proteins that have been retained function in essential core cellular processes such as DNA replication, transcription, and translation [6,8,9]. Proteins that have been lost include many metabolic enzymes, regulatory pathways, and proteins involved in vesicular transport such as TOR (Target of Rapamycin) and clathrin [8-10]. In addition, the proteins that are retained are shorter than their fungal orthologs, with Encephalitozoon cuniculi proteins being on average only 85% as long as their yeast counterparts [3,11]. One such instance of proteins that have decreased in size are the aminoacyl-tRNA synthetases, which have lost many regulatory regions, including a domain in leucyl-tRNA synthetase (LeuRS) that edits mischarged tRNAs. The microsporidia Vavraia culicis was shown to have mistranslation error rates of 5.9% at positions that coded for leucine-although valine, which has a corresponding tRNA synthetases with an intact editing domain, has a mistranslation rate of 7.5%, suggesting that there are other factors responsible for the high levels of mistranslated proteins [12]. Microsporidia also have reduced noncoding RNAs, including the 18s RNA, which is only approximately 2/3 as large as in other eukaryotes and results in the smallest eukaryotic ribosomes [13]. Although this reduction has led to several binding sites being eliminated, structural and mass spectrometry analysis of ribosomes from Vairimorpha necatrix demonstrated

Argonaute (AGO) proteins associate with small RNAs to direct their effector function on complementary transcripts. The nematode Caenorhabditis elegans contains an expanded family of 19 functional AGO proteins, many of which have not been fully characterized. In this work, we systematically analyzed every C. elegans AGO using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG tags. We have characterized the expression patterns of each AGO throughout development, identified small RNA binding complements, and determined the effects of ago loss on small RNA populations and developmental phenotypes. Our analysis indicates stratification of subsets of AGOs into distinct regulatory modules, and integration of our data led us to uncover novel stress-induced fertility and pathogen response phenotypes due to ago loss.

Microsporidia are a large group of parasites that cause death and disease in humans and many agriculturally important animal species. To fully understand the diverse properties of these parasites, we curated species reports from the last 160 years.

Pathogens use a variety of secreted and surface proteins to interact with and manipulate their hosts, but a systematic approach for identifying such proteins has been lacking. To identify these ‘host-exposed’ proteins, we used spatially restricted enzymatic tagging followed by mass spectrometry analysis of Caenorhabditis elegans infected with two species of Nematocida microsporidia. We identified 82 microsporidia proteins inside of intestinal cells, including several pathogen proteins in the nucleus. These microsporidia proteins are enriched in targeting signals, are rapidly evolving and belong to large Nematocida-specific gene families. We also find that large, species-specific families are common throughout microsporidia species. Our data suggest that the use of a large number of rapidly evolving species-specific proteins represents a common strategy for microsporidia to interact with their hosts. The unbiased method described here for identifying potential pathogen effectors represents a powerful approach to study a broad range of pathogens.