Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses

In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been limited to evolutionarily related organisms. The amino acid sequences of histone proteins are highly conserved from humans to yeasts, but are divergent in the deeply branching protozoan groups, including human parasites that are directly related to human health. Certain large DNA viruses, as well as archaeal organisms, contain distant homologs of eukaryotic histone proteins. The divergent sequences give rise to unique and distinct nucleosome architectures, although the fundamental principles of histone folding and DNA contact are highly conserved. In this article, we review the structures and biophysical properties of nucleosomes containing histones from the human parasites Giardia lamblia and Leishmania major, and histone-like proteins from the Marseilleviridae amoeba virus family. The presented data confirm the sharing of the overall DNA compaction system among evolutionally distant species and clarify the deviations from the species-specific nature of the nucleosome.

Method for Evaluating Effects of Non-coding RNAs on Nucleosome Stability

In eukaryotic cells, genomic DNA is stored in the nucleus in a structure called chromatin. The nucleosome, the basic structural unit of chromatin consisting of DNA wound around a histone octamer, regulates access of transcription machinery to DNA. Nucleosome stability is thus tightly associated with gene expression. Recently, a class of non-coding RNAs was found to be directly associated with chromatin. Although these non-coding RNAs are reportedly important in genome regulation, the molecular mechanisms through which these RNAs act remain unclear. Here, we introduce a biochemical method to evaluate the effects of ncRNAs on nucleosome stability, using the breast cancer-associated ncRNA Eleanor2 as an example. This method is useful for assessing the effects of different RNAs on chromatin stability and conformation.

Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones

Giardia lamblia is a pathogenic unicellular eukaryotic parasite that causes giardiasis. Its genome encodes the canonical histones H2A, H2B, H3, and H4, which share low amino acid sequence identity with their human orthologues. We determined the structure of the G. lamblia nucleosome core particle (NCP) at 3.6 Å resolution by cryo-electron microscopy. G. lamblia histones form a characteristic NCP, in which the visible 125 base-pair region of the DNA is wrapped in a left-handed supercoil. The acidic patch on the G. lamblia octamer is deeper, due to an insertion extending the H2B α1 helix and L1 loop, and thus cannot bind the LANA acidic patch binding peptide. The DNA and histone regions near the DNA entry-exit sites could not be assigned, suggesting that these regions are asymmetrically flexible in the G. lamblia NCP. Characterization by thermal unfolding in solution revealed that both the H2A–H2B and DNA association with the G. lamblia H3–H4 were weaker than those for human H3–H4. These results demonstrate the uniformity of the histone octamer as the organizing platform for eukaryotic chromatin, but also illustrate the unrecognized capability for large scale sequence variations that enable the adaptability of histone octamer surfaces and confer internal stability.

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, the RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. Using this method, we found that H3.1 and H3.3 were incorporated into chromatin in replication-dependent and -independent manners, respectively. We further found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition to maintain the epigenetic chromatin states.

Leishmania dual-specificity tyrosine-regulated kinase 1 (DYRK1) is required for sustaining Leishmania stationary phase phenotype

Although the multiplicative and growth-arrested states play key roles in Leishmania development, the regulators of these transitions are largely unknown. In an attempt to gain a better understanding of these processes, we characterised one member of a family of protein kinases with dual specificity, LinDYRK1, which acts as a stasis regulator in other organisms. LinDYRK1 overexpressing parasites displayed a decrease in proliferation and in cell cycle re-entry of arrested cells. Parasites lacking LinDYRK1 displayed distinct fitness phenotypes in logarithmic and stationary growth phases. In logarithmic growth phase, LinDYRK1-/- parasites proliferated better than control lines, supporting a role of this kinase in stasis, while in stationary growth phase, LinDYRK1-/- parasites had important defects as they rounded up, accumulated vacuoles and lipid bodies and displayed subtle but consistent differences in lipid composition. Moreover, they expressed less metacyclic-enriched transcripts, displayed increased sensitivity to complement lysis and a significant reduction in survival within peritoneal macrophages. The distinct LinDYRK1-/- growth phase phenotypes were mirrored by the distinct LinDYRK1 localisations in logarithmic (mainly in flagellar pocket area and endosomes) and late stationary phase (mitochondrion). Overall, this work provides first evidence for the role of a DYRK family member in sustaining promastigote stationary phase phenotype and infectivity.

Incorporation and influence of Leishmania histone H3 in chromatin

Immunopathologies caused by Leishmania cause severe human morbidity and mortality. This protozoan parasite invades and persists inside host cells, resulting in disease development. Leishmania modifies the epigenomic status of the host cells, thus probably averting the host cell defense mechanism. To accomplish this, Leishmania may change the host cell chromatin structure. However, the mechanism by which the parasite changes the host cell chromatin has not been characterized. In the present study, we found that ectopically produced Leishmania histone H3, LmaH3, which mimics the secreted LmaH3 in infected cells, is incorporated into chromatin in human cells. A crystallographic analysis revealed that LmaH3 forms nucleosomes with human histones H2A, H2B and H4. We found that LmaH3 was less stably incorporated into the nucleosome, as compared to human H3.1. Consistently, we observed that LmaH3-H4 association was remarkably weakened. Mutational analyses revealed that the specific LmaH3 Trp35, Gln57 and Met98 residues, which correspond to the H3.1 Tyr41, Arg63 and Phe104 residues, might be responsible for the instability of the LmaH3 nucleosome. Nucleosomes containing LmaH3 resisted the Mg2+-mediated compaction of the chromatin fiber. These distinct physical characteristics of LmaH3 support the possibility that histones secreted by parasites during infection may modulate the host chromatin structure.

Antennal tactile learning in the honeybee: Effect of nicotinic antagonists on memory dynamics

Restrained worker honeybees (Apis mellifera L.) are able to learn to associate antennal-scanning of a metal plate with a sucrose reinforcement delivered to the mouthparts. Learning occurs reliably in a single association of the two sensory stimuli. The involvement of nicotinic pathways in memory formation and retrieval processes was tested by injecting, into the whole brain through the median ocellus, either mecamylamine (0.6 microg per bee) or alpha-bungarotoxin (2.4 ng per bee). Saline served as a control. Mecamylamine injected 10 min before the retrieval test impairs the retention level tested 3 h and 24 h after single- or multi-trial learning. Retrieval tests performed at various times after the injection show that the blocking effect of mecamylamine lasts about 1 h. The drug has no effect on the reconsolidation or extinction processes. Mecamylamine injected 10 min before conditioning impairs single-trial learning but has no effect on five-trial learning and on the consolidation process. By contrast, alpha-bungarotoxin only impairs the formation of long-term memory (24 h) induced by the five-trial learning and has no effect on medium-term memory (3 h), on single-trial learning or on the retrieval process. Hence, owing to previous data, at least two kinds of nicotinic receptors seem to be involved in honeybee memory, an alpha-bungarotoxin-sensitive and an alpha-bungarotoxin-insensitive receptor. Our results extend to antennal mechanosensory conditioning the role of the cholinergic system that we had previously described for olfactory conditioning in the honeybee. Moreover, we describe here in this insect a pharmacological dissociation between alpha-bungarotoxin sensitive long-term memory and alpha-bungarotoxin insensitive medium-term memory, the last one being affected by mecamylamine.

Effect of morphine on caloric intake and macronutrient selection in male and female Lou/c/jall rats during ageing

Previous studies have showed a shift of preferences from carbohydrate to fat in the Lou/c/jall rat with advancing age when they are submitted to a self-selection procedure. Protein intake also decreased according to the age, earlier for males (after 16 months) than for females (29 months). The present study aimed at investigating the mechanism underlying these modifications. We analysed the effect of the reference mu agonist, morphine (5 mg/kg subcutaneous), on the caloric intake, body weight and macronutrient intake of 30 male and 30 female rats divided in four age groups: young adults (10), mature (17), old (24) and senescent rats (29 months). During the experiment, animals had the choice between separate sources of the three pure macronutrients. Morphine injection reduced total daily caloric intake and induced a decrease in body weight. The weight loss was age- and sex-related (males and old rats were more affected by the drugs). The injection of morphine evoked a triphasic influence on the chronology of the intake. A brief (1 h) hypophagia was followed by an hyperphagia (3 h) and a persistent hypophagia (8 h). No modification in the diet composition was observed. These results did not support a clear involvement of the opioid system concerning the modifications in macronutrient rates in diet previously observed across ageing.

Prevalence of psychological impairment in city and country samples

A study was conducted of the psychological health of 125 married French women aged between 35 and 39 years, divided into five professional groups of 25 subjects. Two of these groups were taken from a rural area, three from Paris. The criteria of health have been psychiatric symptomatology, psychological impairment, and the frequency of the periods of impairment. A significant difference was found between the farmers and all the other groups. Differential data are also given regarding the medical assistance received by the groups.