RINGs, DUBs and Abnormal Brain Growth—Histone H2A Ubiquitination in Brain Development and Disease

During mammalian neurodevelopment, signaling pathways converge upon transcription factors (TFs) to establish appropriate gene expression programmes leading to the production of distinct neural and glial cell types. This process is partially regulated by the dynamic modulation of chromatin states by epigenetic systems, including the polycomb group (PcG) family of co-repressors. PcG proteins form multi-subunit assemblies that sub-divide into distinct, yet functionally related families. Polycomb repressive complexes 1 and 2 (PRC1 and 2) modify the chemical properties of chromatin by covalently modifying histone tails via H2A ubiquitination (H2AK119ub1) and H3 methylation, respectively. In contrast to the PRCs, the Polycomb repressive deubiquitinase (PR-DUB) complex removes H2AK119ub1 from chromatin through the action of the C-terminal hydrolase BAP1. Genetic screening has identified several PcG mutations that are causally associated with a range of congenital neuropathologies associated with both localised and/or systemic growth abnormalities. As PRC1 and PR-DUB hold opposing functions to control H2AK119ub1 levels across the genome, it is plausible that such neurodevelopmental disorders arise through a common mechanism. In this review, we will focus on advancements regarding the composition and opposing molecular functions of mammalian PRC1 and PR-DUB, and explore how their dysfunction contributes to the emergence of neurodevelopmental disorders

Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis, revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event

Adaptive plasticity in the gametocyte conversion rate of malaria parasites

<div><p>Sexually reproducing parasites, such as malaria parasites, experience a trade-off between the allocation of resources to asexual replication and the production of sexual forms. Allocation by malaria parasites to sexual forms (the conversion rate) is variable but the evolutionary drivers of this plasticity are poorly understood. We use evolutionary theory for life histories to combine a mathematical model and experiments to reveal that parasites adjust conversion rate according to the dynamics of asexual densities in the blood of the host. Our model predicts the direction of change in conversion rates that returns the greatest fitness after perturbation of asexual densities by different doses of antimalarial drugs. The loss of a high proportion of asexuals is predicted to elicit increased conversion (terminal investment), while smaller losses are managed by reducing conversion (reproductive restraint) to facilitate within-host survival and future transmission. This non-linear pattern of allocation is consistent with adaptive reproductive strategies observed in multicellular organisms. We then empirically estimate conversion rates of the rodent malaria parasite <i>Plasmodium chabaudi</i> in response to the killing of asexual stages by different doses of antimalarial drugs and forecast the short-term fitness consequences of these responses. Our data reveal the predicted non-linear pattern, and this is further supported by analyses of previous experiments that perturb asexual stage densities using drugs or within-host competition, across multiple parasite genotypes. Whilst conversion rates, across all datasets, are most strongly influenced by changes in asexual density, parasites also modulate conversion according to the availability of red blood cell resources. In summary, increasing conversion maximises short-term transmission and reducing conversion facilitates in-host survival and thus, future transmission. Understanding patterns of parasite allocation to reproduction matters because within-host replication is responsible for disease symptoms and between-host transmission determines disease spread.</p></div

Spatial regulation of microtubule-associated proteins by 14-3-3 in oocytes

Oocytes have a large volume and yet must assemble a bipolar meiotic spindle specifically around the chromosomes. Recently, 14-3-3 was discovered to spatially regulate the spindle assembly factor Kinesin-14/Ncd in fly oocytes. 14-3-3 is also known to spatially regulate another kinesin, Mklp1/Pavarotti, in mitosis. I hypothesise that other meiotic targets of this regulatory pathway may also exist. To test this, I established a new method to cosediment microtubules and associated proteins (MAPs) from fly ovaries. I discovered that over fifty proteins significantly changed in their microtubule-binding activity when 14-3-3 was inhibited in this assay. As well as the two previously reported 14-3-3 interactors, I identified candidate proteins to test for 14-3-3 regulation, including the CPC (chromosomal passenger complex) components Borealin and Incenp, and seven candidates not previously known to have a role in oocyte meiosis. By expressing shRNA against the seven candidates without known meiotic function, I identified five which produced spindle or oogenesis defects, suggesting that they may have a role in spindle assembly in oocytes. Slender Lobes protein localised to the spindle in live imaging, and RNAi of slender lobes led to spindle pole focusing defects. Similarly, the microtubule depolymeriser Stathmin may be required for spindle bipolarity. Borealin is already known to have a role in targeting CPC at the spindle. I identified a candidate 14-3-3 binding site in Borealin with similarity to those of Ncd and Pavarotti. In vitro pulldowns showed that 14-3-3 binds this region of Borealin in a phosphorylation-dependent manner, and that this binding is inhibited by Aurora B phosphorylation, in keeping with the proposed model for 14-3-3 regulation of Ncd. Additionally, I found that this region of Borealin is competent to bind microtubules in vitro, independent of its previously reported microtubule-binding site or interaction with other members of the CPC. Finally, a mutation of this binding site caused the decreased localisation of Borealin to the spindle and centromeres, and chromosome biorientation defects in oocytes. Overall, I propose that 14-3-3 is an important regulator of spindle assembly in oocytes, by spatially regulating microtubule binding of multiple spindle MAPs

The phospho-docking protein 14-3-3 regulates microtubule-associated proteins in oocytes including the chromosomal passenger Borealin

Global regulation of spindle-associated proteins is crucial in oocytes due to the absence of centrosomes and their very large cytoplasmic volume, but little is known about how this is achieved beyond involvement of the Ran-importin pathway. We previously uncovered a novel regulatory mechanism in Drosophila oocytes, in which the phospho-docking protein 14-3-3 suppresses microtubule binding of Kinesin-14/Ncd away from chromosomes. Here we report systematic identification of microtubule-associated proteins regulated by 14-3-3 from Drosophila oocytes. Proteins from ovary extract were co-sedimented with microtubules in the presence or absence of a 14-3-3 inhibitor. Through quantitative mass-spectrometry, we identified proteins or complexes whose ability to bind microtubules is suppressed by 14-3-3, including the chromosomal passenger complex (CPC), the centralspindlin complex and Kinesin-14/Ncd. We showed that 14-3-3 binds to the disordered region of Borealin, and this binding is regulated differentially by two phosphorylations on Borealin. Mutations at these two phospho-sites compromised normal Borealin localisation and centromere bi-orientation in oocytes, showing that phospho-regulation of 14-3-3 binding is important for Borealin localisation and function

Adaptive plasticity in the gametocyte conversion rate of malaria parasites

Malaria parasites in the host replicate asexually and, during each replication cycle, some asexuals transform into sexual stages that enable between-host transmission. It is not understood why the rate of conversion to sexual stages varies during infections despite its importance for the severity and spread of the disease. We combined a mathematical model and experiments to show that parasites adjust conversion rates depending on changes in their in-host population size. When population sizes plummet, between-host transmission is prioritised. However, smaller losses in number elicit reproductive restraint, which facilitates in-host survival and future transmission. We show that increased and decreased conversion in response to a range of in-host environments are actually part of one continuum: a sophisticated reproductive strategy similar to that of multicellular organisms.Schneider, Petra; Greischar, Megan A; Birget, Philip L G; Repton, Charlotte; Mideo, Nicole; Reece, Sarah E. (2018). Adaptive plasticity in the gametocyte conversion rate of malaria parasites, [dataset]. University of Edinburgh. https://doi.org/10.7488/ds/2460

Supplementary Material from Phenotypic plasticity in reproductive effort: malaria parasites respond to resource availability

contains details of initial experiments, statistical tests and additional figures

For_DRYAD

The file is a zip archive of four files: Wolbachia_phylogenomic_90genes_concatenate.faa (the catenated aminoacid alignemtn of 90 genes), Wolbachia_phylogenomic_90genes_concatenate.ffn (the catenated nucleic acid alignemtn of 90 genes), Wolbachia_phylogenomic_OrthoMCL_cluster_aminoacidic_multifastas.zip (a zip file of the amino acid/protein sequences of clusters generated from the Wolbachia genomes using orthoMCL) and Wolbachia_phylogenomic_OrthoMCL_cluster_nucleotidic_multifastas.zip (a zip file of the nucleic acid sequences of clusters generated from the Wolbachia genomes using orthoMCL