1.688 g/cm3 satellite‐related repeats: a missing link to dosage compensation and speciation

Despite the important progress that has been made on dosage compensation (DC), a critical link in our understanding of the X chromosome recognition mechanisms is still missing. Recent studies in Drosophila indicate that the missing link could be a family of DNA repeats populating the euchromatin of the X chromosome. In this opinion article, I discuss how these findings add a new fresh twist on the DC problem. In the following sections, I first summarize our understanding of DC in Drosophila and integrate these recent discoveries into our knowledge of the X chromosome recognition problem. Next, I introduce a model according to which, 1.688 g/cm³ satellite‐related (SR) repeats would be the primary recognition elements for the dosage compensation complex. Contrary to the current belief, I suggest that the DC system in Drosophila is not conserved and static, but it is continuously co‐evolving with the target SR repeats. The potential role of the SR repeats in hybrid incompatibilities and speciation is also discussed.     

Mass spectrometry based analysis of human plasma‐derived factor X revealed novel post‐translational modifications

Human coagulation factor X is a central component of the blood coagulation cascade that converts, under its activated form, prothrombin into thrombin. Generation of thrombin is the final step of the clotting cascade that leads to the clot by polymerization of fibrinogen molecules into a fibrin network. Today, research of new by‐passing agents of the coagulation may contribute to an increased interest for human factor X, which may, in consequence, lead to the need of a more exhaustive picture of its structural features. Several post‐translational modifications of human factor X such as γ‐carboxylation/β‐hydroxylation of the N‐terminal light chain and N‐/O‐glycosylation of the activation peptide have been described. But, so far as we know, no comprehensive studies of its post‐translational modifications have been reported. In this article we report an exhaustive structural analysis of human factor X by mass spectrometry using successive protein and peptide mapping. Surprisingly, human factor X was found to be mostly O‐glucosylated on its light chain at Ser₁₀₆ position, Ser₉ of its activation peptide is phosphorylated at about 30% and its C‐terminal heavy chain is fully O‐glycosylated at Thr₂₄₉ by a mucin‐type O‐glycan (HexNAc‐Hex‐NeuAc). The knowledge of these post‐translational modifications is mandatory for the development of recombinant molecules.     

The crystal structure of the catalytic domain of the ser/thr kinase PknA from M. tuberculosis shows an Src‐like autoinhibited conformation

Signal transduction mediated by Ser/Thr phosphorylation in Mycobacterium tuberculosis has been intensively studied in the last years, as its genome harbors eleven genes coding for eukaryotic‐like Ser/Thr kinases. Here we describe the crystal structure and the autophosphorylation sites of the catalytic domain of PknA, one of two protein kinases essential for pathogen's survival. The structure of the ligand‐free kinase domain shows an auto‐inhibited conformation similar to that observed in human Tyr kinases of the Src‐family. These results reinforce the high conservation of structural hallmarks and regulation mechanisms between prokaryotic and eukaryotic protein kinases. Proteins 2015; 83:982–988. © 2015 Wiley Periodicals, Inc.     

Heteromerous Bistricyclic Aromatic Enes: Dynamic Stereochemistry of Xanthylidene‐Anthrones

The heteromerous bistricyclic aromatic ene (BAE) 2,2'‐dimethyl‐10‐(9H‐xanthylidene)‐9(10H)‐anthrone (DMXA) was synthesized by a condensation of 10,10‐dichloro‐2‐methylxanthene with 2‐methylanthrone. X‐ray crystallography of (E)‐DMXA and xanthylidene‐anthrone (XA) indicated that the molecules adopt anti‐folded conformations with folding dihedral angles of 44°/44° and 39°/41°, respectively . The crystal structure of anti‐folded (E)‐DMXA does not indicate any xanthenylium–anthracenolate push–pull effect. E,Z‐diastereomerization of DMXA was studied by ¹H‐NMR coalescence‐temperature measurements at different magnetic field strengths and by kinetic equilibration experiments . Free energy of activation for this process was 81.5 (±1.3) kJ/mol. B3LYP/6‐311+G(d,p) calculations showed that anti‐folded conformers of XA, (E)‐DMXA, bianthrone (AA), and dixanthylene (XX) were global minima. The twisted conformers of XA, AA, and XX were local minima (ΔG₂₉₈ = 16, 18, and 24 kJ/mol) with a substantial dipolar xanthenylium–anthracenolate dipolar contribution for XA. Chirality 27:919–928, 2015. © 2015 Wiley Periodicals, Inc.     

Theoretical studies on interaction of anticancer drugs (dacarbazine,procarbazine and triethylenemelamine) with normal (AT and GC) and mismatch (GG,CC, AA and TT) base pairs

This study is an attempt to gain a better understanding of the physicochemical interaction between novel anticancer drugs and DNA bases. We have employed quantum chemical tools to explore the interaction of a few anticancer drugs [namely procarbazine (PR), dacarbazine (DC) and triethylenemelamine (TR)] with isolated normal (GC and AT) and mismatch (AA, CC, GG and TT) base pairs. The molecular geometries, electronic structural stability, vibrational energies, chemical reactivity and other electronic properties were studied using MP2/6-311+G^**, B3LYP/6-311+G^** and M05-2X/6-311+G^** methods. The optimised geometries of the usual and mismatch base pairs are almost planar whereas the geometries of drug-interacting complexes deviate from planarity. The presence of steric hindrance and π-bond overlaps between C–C bonds in the complexes has distorted the planarity of the four- and five-member rings in the base pairs. Among the three drugs chosen, DC and PR bond well with normal and mismatch base pairs with large interaction energy. The electron density (ED) difference maps of the most stable GG–DC, GG–PR and GG–TR drug-interacting complexes show the information about sharing of ED and gain or loss of ED within the interacting molecules. The stabilisation energy of the charge transfer interaction between the relevant donor–acceptor orbital of GG–DC and GC–DC complexes has been found to be around 16 kcal/mol and GG–PR and GC–PR complexes has been found to be around 12 kcal/mol. But, for the GG–TR and GC–TR complexes, the stabilisation energy is found to be less than 6 kcal/mol. Moreover, the topological analysis of hydrogen bond network of DC and PR drug-interacting complexes have high electron and Laplacian density with structural stability at the bond critical points (BCPs), while compared TR drug-interacting complexes by atoms in molecules and natural bond orbital analysis. Finally, we may conclude that the drugs DC and PR are highly efficient drugs to target normal and mismatch base pair for control and inhibition of DNA replication.     

Differential contributions of plant Dicer‐like proteins to antiviral defences against potato virus X in leaves and roots

Members of the plant Dicer‐like (DCL) protein family are the critical components of the RNA‐silencing pathway that mediates innate antiviral defence. The distinct antiviral role of each individual DCL protein has been established with mostly based on observations of aerial parts of plants. Thus, although the roots are closely associated with the life cycle of many plant viruses, little is known about the antiviral activities of DCL proteins in roots. We observed that antiviral silencing strongly inhibits potato virus X (PVX) replication in roots of some susceptible Solanaceae species. Silencing of the DCL4 homolog in Nicotiana benthamiana partially elevated PVX replication levels in roots. In Arabidopsis thaliana, which was originally considered a non‐host plant of PVX, high levels of PVX accumulation in inoculated leaves were achieved by inactivation of DCL4, while in the upper leaves and roots, it required the additional inactivation of DCL2. In transgenic A. thaliana carrying the PVX amplicon with a green fluorescent protein (GFP) gene insertion in the chromosome (AMP243 line), absence of DCL4 enabled high levels of PVX‐GFP accumulation in various aerial organs but not in the roots, suggesting that DCL4 is critical for intracellular antiviral silencing in shoots but not in roots, where it can be functionally compensated by other DCL proteins. Together, the high level of functional redundancies among DCL proteins may contribute to the potent antiviral activities against PVX replication in roots.     

非酒精性脂肪性肝病与代谢综合征组分的相关性研究进展

非酒精性脂肪性肝病(nonalcoholic fatty liver disease,NAFLD)在全世界人群中发病率逐年上升,成为新的全球公共健康问题,已越来越引起临床关注。其发病以胰岛素抵抗为基础,与肥胖、血脂紊乱、原发性高血压、2型糖尿病等代谢综合征各组分密切相关。NAFLD可进展至肝硬化、肝衰竭甚至肝癌,伴有代谢综合征一种或多种组分可能加速疾病的进展。NAFLD初期是一种可逆性过程,充分了解影响其发生、发展的相关代谢危险因素并及时纠正,可能导致疾病的逆转或延缓其进程。本文就NAFLD与代谢综合征各组分的相关调查研究进行综述。     

Homodimerization propensity of the intrinsically disordered N-terminal domain of Ultraspiracle from Aedes aegypti

The mosquito Aedes aegypti is the principal vector of dengue, one of the most devastating arthropod-borne viral infections in humans. The isoform specific A/B region, called the N-terminal domain (NTD), is hypervariable in sequence and length and is poorly conserved within the Ultraspiracle (Usp) family. The Usp protein together with ecdysteroid receptor (EcR) forms a heterodimeric complex. Up until now, there has been little data on the molecular properties of the isolated Usp-NTD. Here, we describe the biochemical and biophysical properties of the recombinant NTD of the Usp isoform B (aaUsp-NTD) from A. aegypti. These results, in combination with in silico bioinformatics approaches, indicate that aaUsp-NTD exhibits properties of an intrinsically disordered protein (IDP). We also present the first experimental evidence describing the dimerization propensity of the isolated NTD of Usp. These characteristics also appear for other members of the Usp family in different species, for example, in the Usp-NTD from Drosophila melanogaster and Bombyx mori. However, aaUsp-NTD exhibits the strongest homodimerization potential. We postulate that the unique dimerization of the NTD might be important for Usp function by providing an additional platform for interactions, in addition to the nuclear receptor superfamily dimerization via DNA binding domains and ligand binding domains that has already been extensively documented. Furthermore, the unique NTD–NTD interaction that was observed might contribute new insight into the dimerization propensities of nuclear receptors.     

P2X receptors regulate adenosine diphosphate release from hepatic cells

Extracellular nucleotides act as paracrine regulators of cellular signaling and metabolic pathways. Adenosine polyphosphate (adenosine triphosphate (ATP) and adenosine diphosphate (ADP)) release and metabolism by human hepatic carcinoma cells was therefore evaluated. Hepatic cells maintain static nanomolar concentrations of extracellular ATP and ADP levels until stress or nutrient deprivation stimulates a rapid burst of nucleotide release. Reducing the levels of media serum or glucose has no effect on ATP levels, but stimulates ADP release by up to 10-fold. Extracellular ADP is then metabolized or degraded and media ADP levels fall to basal levels within 2–4 h. Nucleotide release from hepatic cells is stimulated by the Ca²⁺ ionophore, ionomycin, and by the P2 receptor agonist, 2′3′-O-(4-benzoyl-benzoyl)-adenosine 5′-triphosphate (BzATP). Ionomycin (10 μM) has a minimal effect on ATP release, but doubles media ADP levels at 5 min. In contrast, BzATP (10–100 μM) increases both ATP and ADP levels by over 100-fold at 5 min. Ion channel purinergic receptor P2X7 and P2X4 gene silencing with small interference RNA (siRNA) and treatment with the P2X inhibitor, A438079 (100 μM), decrease ADP release from hepatic cells, but have no effect on ATP. P2X inhibitors and siRNA have no effect on BzATP-stimulated nucleotide release. ADP release from human hepatic carcinoma cells is therefore regulated by P2X receptors and intracellular Ca²⁺ levels. Extracellular ADP levels increase as a consequence of a cellular stress response resulting from serum or glucose deprivation.

Electronic supplementary material

The online version of this article (doi:10.1007/s11302-014-9419-2) contains supplementary material, which is available to authorized users.