REELIN and schizophrenia: a disease at the interface of the genome and the epigenome

The downregulation of the Reelin gene (RELN) that occurs in schizophrenic brains, which are characterized by pyramidal neurons with shortened dendrites and by reduced expression densities of dendritic spines, may well result from hypermethylation of the RELN promoter. In the adult mammalian brain, gamma-aminoburytic acid-secreting (GABAergic) interneurons release RELN into the extracellular matrix, where it binds with high affinity to the integrin receptors present at dendritic spine postsynaptic densities and likely plays a role, elaborated in this article, in synaptic plasticity. In heterozygous reeler mice, which are haploinsufficient in RELN, inhibitors of histone deacetylase increase DNA demethylase activity and restore RELN expression. Such inhibitors could thus be of therapeutic value in mitigating vulnerability to schizophrenia among high-risk individuals.     

Structural bistability of the GAL regulatory network and characterization of its domains of attraction

Bistability is a system-level property, exploited by many biomolecular interaction networks as a key mechanism to accomplish different cellular functions (e.g., differentiation, cell cycle, switch-like response to external stimuli). Bistability has also been experimentally found to occur in the regulatory network of the galactose metabolic pathway in the model organism Saccharomyces cerevisiae. In this yeast, bistability generates a persistent memory of the type of carbon source available in the extracellular medium: under the same experimental conditions, cells previously grown with different nutrients generate different responses and get stably locked into two distinct steady states. The molecular interactions of the GAL regulatory network have been thoroughly dissected through wet-lab experiments; thus, this system provides a formidable benchmark to our ability to characterize and reproduce in silico the behavior of bistable biological systems. To this aim, a number of models have been proposed in the literature; however, we found that they are not able to replicate the persistent memory behavior observed in (Acar et al., 2005 ). The present study proposes a novel model of the GAL regulatory network, which, in addition to reproducing in silico the experimental findings, can be formally analyzed for structural multistability of the network, using chemical reaction network theory (CRNT), and allows the characterization of the domains of attraction (DA). This work provides further insights into the GAL system and proposes an easily generalizable approach to the study of bistability-associated behaviors in biological systems.     

Structural microbiology at the pathogen-host interface

Bacterial pathogens achieve the internalization of a multitude of virulence factors into eukaryotic cells. Some secrete extracellular toxins which bring about their own entry, usually by hijacking cell surface receptors and endocytic pathways. Others possess specialized secretion and translocation systems to directly inject bacterial proteins into the host cytosol. Recent advances in the structural biology of these virulence factors has begun to reveal at the molecular level how these bacterial proteins are delivered and modulate host activities ranging from cytoskeletal structure to cell cycle progression.     

The epigenome of Trypanosoma brucei: A regulatory interface to an unconventional transcriptional machine

The epigenome represents a major regulatory interface to the eukaryotic genome. Nucleosome positions, histone variants, histone modifications and chromatin associated proteins all play a role in the epigenetic regulation of DNA function.     

Observations at the interface of mutation research and regulatory policy

Between 1970 and 1975 developments in environmental mutagenesis proceeded with amazing speed. These developments were both structural and conceptual in nature. A new infrastructure was built and new concepts about how best to protect consumers from exposures to mutagens emerged. The internal dynamics within the Food and Drug Administration played an important role and is discussed with regard to modifications in testing protocols as well as changes in the overall approach used to protect consumers. It is clear that this exciting period in the early days of environmental mutagenesis has provided a base for growth and development of the field and continues to affect and guide future developments.     

Structural basis for catalysis at the membrane-water interface

The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments – the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.     

Type 3 regulatory T cells at the interface of symbiosis

The mammalian gastrointestinal tract accommodates trillions of bacteria, many of which provide beneficial effects to the host, including protection from pathogenic microorganisms and essential metabolites. However, the intestinal immune system needs to adapt to the constantly fluctuating microbial environment at mucosal surfaces in order to maintain homeostasis. In particular, the gut microbiota induces the differentiation of effector Th17 cells and regulatory T cells (Tregs) that express RORγt, the master regulator of antimicrobial type 3 immunity. RORγt⁺ Tregs constitute a major population of colonic Tregs that is distinct from thymusderived Tregs and require bacterial antigens for differentiation. The balance between Th17 cells and RORγt⁺ Tregs, that is, the tone of the local type 3 immune response, is regulated by the vitamin A metabolite retinoic acid produced by the host. Furthermore, Th17 cells and RORγt⁺ Tregs regulate intestinal type 2 immune responses, explaining how bacteria block allergic reactions. Here, we review the cellular and molecular mechanisms involved in the differentiation, regulation and function of RORγt⁺ (type 3) Tregs, and discuss the multiple equilibria that exist between effector T cells and Tregs, as well as between different types of immune responses, which are necessary to maintain homeostasis and health.     

Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface

Beta-lactamase inhibitor protein (BLIP) binds a variety of class A beta-lactamases with affinities ranging from micromolar to picomolar. Whereas the TEM-1 and SHV-1 beta-lactamases are almost structurally identical, BLIP binds TEM-1 approximately 1000-fold tighter than SHV-1. Determining the underlying source of this affinity difference is important for understanding the molecular basis of beta-lactamase inhibition and mechanisms of protein-protein interface specificity and affinity. Here we present the 1.6A resolution crystal structure of SHV-1.BLIP. In addition, a point mutation was identified, SHV D104E, that increases SHV.BLIP binding affinity from micromolar to nanomolar. Comparison of the SHV-1.BLIP structure with the published TEM-1.BLIP structure suggests that the increased volume of Glu-104 stabilizes a key binding loop in the interface. Solution of the 1.8A SHV D104K.BLIP crystal structure identifies a novel conformation in which this binding loop is removed from the interface. Using these structural data, we evaluated the ability of EGAD, a program developed for computational protein design, to calculate changes in the stability of mutant beta-lactamase.BLIP complexes. Changes in binding affinity were calculated within an error of 1.6 kcal/mol of the experimental values for 112 mutations at the TEM-1.BLIP interface and within an error of 2.2 kcal/mol for 24 mutations at the SHV-1.BLIP interface. The reasonable success of EGAD in predicting changes in interface stability is a promising step toward understanding the stability of the beta-lactamase.BLIP complexes and computationally assisted design of tight binding BLIP variants.     

Structural characterization of the regulatory domain of brain carnitine palmitoyltransferase 1

Neurons contain a mammalian‐specific isoform of the enzyme carnitine palmitoyltransferase 1 (CPT1C) that couples malonyl‐CoA to ceramide levels thereby contributing to systemic energy homeostasis and feeding behavior. In contrast to CPT1A, which controls the rate‐limiting step of long‐chain fatty acid β‐oxidation in all tissues, the biochemical context and regulatory mechanism of CPT1C are unknown. CPT1 enzymes are comprised of an N‐terminal regulatory domain and a C‐terminal catalytic domain (CD) that are separated by two transmembrane helices. In CPT1A, the regulatory domain, termed N, adopts an inhibitory and non‐inhibitory state, Nα and Nβ, respectively, which differ in their association with the CD. To provide insight into the regulatory mechanism of CPT1C, we have determined the structure of its regulatory domain (residues Met1‐Phe50) by NMR spectroscopy. In relation to CPT1A, the inhibitory Nα state was found to be structurally homologues whereas the non‐inhibitory Nβ state was severely destabilized, suggesting a change in overall regulation. The destabilization of Nβ may contribute to the low catalytic activity of CPT1C relative to CPT1A and makes its association with the CD unlikely. In analogy to the stabilization of Nβ by the CPT1A CD, non‐inhibitory interactions of N of CPT1C with another protein may exist. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 398–405, 2014.     

Structural dynamics of double-stranded DNA with epigenome modification

Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of DNA is known to affect the binding of proteins to methylated DNA. Here, we have carried out a semi-quantitative analysis of the dynamics of double-stranded DNA (dsDNA) containing various epigenetic modifications by combining data from imino ¹H exchange and imino ¹H R_1ρ relaxation dispersion NMR experiments in a complementary way. Using this approach, we characterized the base-opening (k_open) and base-closing (k_close) rates, facilitating a comparison of the base-opening and -closing process of dsDNA containing cytosine in different states of epigenetic modification. A particularly striking result is the increase in the k_open rate of hemi-methylated dsDNA 5mC/C relative to unmodified or fully methylated dsDNA, indicating that the Watson–Crick base pairs undergo selective destabilization in 5mC/C. Collectively, our findings imply that the epigenetic modulation of cytosine dynamics in dsDNA mediates destabilization of the GC Watson–Crick base pair to allow base-flipping in living cells.     

An atlas of the epstein-barr virus transcriptome and epigenome reveals host-virus regulatory interactions

Epstein-Barr virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration.     

Structural characterization of a dimerization interface in the CD28 transmembrane domain

1. Download : Download high-res image (208KB)
2. Download : Download full-size image

     

Structural study of the DNA dipalmitoylphosphatidylcholine complex at the air-water interface

We present here results that demonstrate the formation of a complex of DNA with zwitterionic dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface in the presence of Ca2+ ions; in particular, we show that the presence of Ca2+ cations is essential for the formation of the complex of DPPC with DNA. We characterize the resulting structure by X-ray reflectivity and by null-ellipsometry. We show that DNA maintains its native double helix form when attached to the zwitterionic lipid monolayer, at difference with the case of ammine containing monolayers. Our findings are discussed in view of other works that recently appeared on the interaction of DNA with zwitterionic phospholipids, emphasizing the role of DPPC as a potential vector for transfer of genetic material into mammalian cells by nonviral gene therapy and also suggesting Langmuir/Blodgett layers of zwitterionic phospoholipids as a method for nonconventional DNA immobilization.     

Maternal n-3 PUFA deficiency alters uterine artery remodeling and placental epigenome in the mice

The maternal n-3 polyunsaturated fatty acid (PUFA) deficiency on decidual vascular structure and angiogenesis in mice placenta was investigated. Namely, we studied uterine artery remodeling, fatty acid metabolism, and placental epigenetic methylation in this animal model. Weanling female Swiss albino mice were fed either alpha-linolenic acid (18:3 n-3, ALA) deficient diets (0.13% energy from ALA) or a sufficient diet (2.26% energy from ALA) throughout the study. The dietary n-3 PUFA deficiency altered uteroplacental morphology and vasculature by reversing luminal to vessel area and increased luminal wall thickness at 8.5-12.5gD. Further, placentas (F0 and F1) showed a significant decrease in the expression of VCAM1, HLAG proteins and an increase in MMP9, KDR expression. The conversion of ALA to long-chain (LC) n-3 PUFAs was significantly decreased in plasma and placenta during the n-3 deficiency state. Reduced n-3 LCPUFAs increased the placental expression of intracellular proteins FABP3, FABP4, and ADRP to compensate decreased availability of these fatty acids in the n-3 deficient mice. The N-3 PUFA deficiency significantly increased the 5-methylcytosine levels in the placenta but not in the liver. The alteration in DNA methylation continued to the next generation in the placental epigenome with augmented expression of DNMT3A and DNMT3B. Our study showed that maternal n-3 PUFA deficiency alters placental vascular architecture and induces epigenetic changes suggesting the importance of n-3 PUFA intake during the development of the fetus. Moreover, the study shows that the placenta is the susceptible target for epigenetic alteration in maternal deficiency n-3 fatty acids.     

Structural response to mutation at a protein-protein interface

We have crystallised three mutants of the barnase-barstar complex in which interactions across the interface have been deleted by simultaneous mutation of both residues involved in the interaction. Each mutant deletes a different type of interaction at the interface: the first complex bnHis102-->Ala-bsTyr29-->Phe (bn, barnase; bs, barstar), deletes a van der Waals packing interaction; the second complex, bnLys27-->Ala-bsThr42-->Ala, deletes a hydrogen bond; the third, bnLys27-->Ala-bsAsp35-->Ala, deletes a long-range charge-charge interaction. The contribution of each of these side-chains to the stability of the complex is known; the coupling energy between the deleted side-chains is also known. Despite each of the double mutants being significantly destabilised compared with the wild-type, the effects of mutation are local. Only small movements in the main-chain surrounding the sites of mutation and some larger movements of neighbouring side-chains are observed in the mutant complexes. The exact response to mutation is context-dependent and for the same mutant can vary depending upon the environment within the crystal. In some double mutant complexes, interfacial pockets, which are accessible to bulk solvent are formed, whereas interfacial cavities which are isolated from bulk solvent, are formed in others. In all double mutants, water molecules fill the created pockets and cavities. These water molecules mimic the deleted side-chains by occupying positions close to the non-carbon atoms of truncated side-chains and re-making many hydrogen bonds made by the truncated side-chains in the wild-type. It remains extremely difficult, however, to correlate energetic and structural responses to mutation because of unknown changes in entropy and entropy-enthalpy compensation.