Nucleosome-like Complex of the Histone from the Hyperthermophile Methanopyrus Kandleri (MkaH) with Linear DNA

Abstract

The MkaH protein from the archaeon Methanopyrus kandleri, an unusual assembly of two histone-fold domains in a single polypeptide chain, demonstrates high structural similarity to eukaryal histones. We studied the DNA binding and self-association properties of MkaH by means of the electrophoretic mobility shift assay (EMSA), electron microscopy (EM), chemical cross-linking, and analytical gel filtration. EMSA showed an increased mobility of linear DNA complexed with MkaH protein with a maximum at a protein-DNA weight ratio (Rw) of ≈3; the mobility decreased at higher protein concentration. EM of the complexes formed at Rw ≤ 3 revealed formation of isometric loops encompassing 71 +/- 7 bp of DNA duplex. At high values of Rw (≥9) thickened compact nucleoprotein structures were observed; no individual loops were seen within the complexes. Gel filtration chromatography and chemical fixation indicated that in the absence of DNA the dominant form of the MkaH in solution, unlike other archaeal histones, is a stable dimer (pseudo-tetramer of the histone-fold domain) apparently resembling the eukaryal (H3-H4)₂ tetramer. Similarly, dimers are the dominant form of the protein interacting with DNA. The properties of MkaH supporting the assignment of its intermediate position between other archaeal and eukaryal histones are discussed.     

Structural basis for cytokinin receptor signaling: an evolutionary approach

Cytokinins are ubiquitous plant hormones; their signal is perceived by sensor histidine kinases—cytokinin receptors. This review focuses on recent advances on cytokinin receptor structure, in particular sensing module and adjacent domains which play an important role in hormone recognition, signal transduction and receptor subcellular localization. Principles of cytokinin binding site organization and point mutations affecting signaling are discussed. To date, more than 100 putative cytokinin receptor genes from different plant species were revealed due to the total genome sequencing. This allowed us to employ an evolutionary and bioinformatics approaches to clarify some new aspects of receptor structure and function. Non-transmembrane areas adjacent to the ligand-binding CHASE domain were characterized in detail and new conserved protein motifs were recovered. Putative mechanisms for cytokinin-triggered receptor activation were suggested.     

Morphology of the jaw apparatus in 8 species of Patellogastropoda (Mollusca, Gastropoda) with special reference to Testudinalia tesulata (Lottiidae)

The fine structure of the jaw apparatus was studied by scanning electron microscopy in eight species of Patellogastropoda. The jaw apparatus is an unpaired two-layered dorsolateral structure with anterior and posterior wings attached to the odontophore by muscles. The jaw of Testudinalia tesulata (O.F. Müller, 1776) is a derivative of the cuticle typical for the foregut. The tissue forming the jaw is a specialized foregut epithelium (gnathoepithelium), consisting of a special type of cells called gnathoblasts. The jaw grows in areas of the epithelium characterized by high concentration of electron-dense vesicles, ER and long microvilli that penetrate deep into the jaw plate. This indicates that the gnathoblasts take an active part in jaw growth. In most cases, these areas of the gnathoepithelium are highly folded. The main differences between the species studied are form and thickness of the frontal edge of the jaw. These differences do not correlate with the systematic position of the species studied but likely depend more on the feeding mode. The transmission electron microscopy studies yielded new morphological criteria for comparison between various gastropod species and other members of Trochozoa, in particular, Annelida. The jaws of Annelida are cuticular structures formed on the surface of specialized epithelial cells, often also called gnathoblasts. The jaw of Patellogastropoda can be attributed to the first type of annelid jaw formation characterized by an epithelium with long microvilli and continuous growth.     

Modeling of Peptides in Implicit Membrane-Mimetic Media

Abstract

Lipid bilayer plays a crucial role in folding of membrane peptides and their stabilization in the membrane-bound state. Correct treatment of the media effects is thus essential for realistic simulations of peptides in bilayers. Previously (Volynsky et al., 1999), we proposed an efficient solvation model which mimics heterogeneous membrane-water system. The model is based on combined employment of atomic solvation parameters for water and hydrocarbon, which approximate hydrated headgroups and acyl chains of lipids, respectively. In this study, the model is employed in non-restrained Monte Carlo simulations of several peptides: totally apolar 20-residue poly-L-Leu, hydrophobic peptide with polar edges, and strongly amphiphilic pep-tide. The principal goals are: to explore energy landscape of these peptides in membrane; to characterize the structures of low-energy states and their orientations with respect to the bilayer. Simulations were performed starting from different structures (unordered or helical) and orientations. It was found that the membrane environment significantly promotes an α-helical conformation for all the peptides, while their energetically favourable orientations are quite different. Thus, poly-Leu was immobilized inside the membrane, the hydrophobic peptide with polar termini adapted transbilayer orientation, whereas the amphiphilic peptide stayed on the lipid-water interface in peripherial orientation. Energy barriers between different states were characterized. The computational results were compared with the experimental structural data.     

Coagulation Factor Binding Orientation and Dimerization May Influence Infectivity of Adenovirus-Coagulation Factor Complexes

Adenoviruses (Ads) are promising vectors for therapeutic interventions in humans. When injected into the bloodstream, Ad vectors can bind several vitamin K-dependent blood coagulation factors, which contributes to virus sequestration in the liver by facilitating transduction of hepatocytes. Although both coagulation factors FVII and FX bind the hexon protein of human Ad serotype 5 (HAdv5) with a very high affinity, only FX appears to play a role in mediating Ad-hepatocyte transduction in vivo. To understand the discrepancy between efficacy of FVII binding to hexon and its apparently poor capacity for supporting virus cell entry, we analyzed the HAdv5-FVII complex by using high-resolution cryo-electron microscopy (cryo-EM) followed by molecular dynamic flexible fitting (MDFF) simulations. The results indicate that although hexon amino acids T423, E424, and T425, identified earlier as critical for FX binding, are also involved in mediating binding of FVII, the FVII GLA domain sits within the surface-exposed hexon trimer depression in a different orientation from that found for FX. Furthermore, we found that when bound to hexon, two proximal FVII molecules interact via their serine protease (SP) domains and bury potential heparan sulfate proteoglycan (HSPG) receptor binding residues within the dimer interface. In contrast, earlier cryo-EM studies of the Ad-FX interaction showed no evidence of dimer formation. Dimerization of FVII bound to Ad may be a contributing mechanistic factor for the differential infectivity of Ad-FX and Ad-FVII complexes, despite high-affinity binding of both these coagulation factors to the virus.     

Regulatory role of membrane fluidity in gene expression and physiological functions

Plants, algae, and photosynthetic bacteria experience frequent changes in environment. The ability to survive depends on their capacity to acclimate to such changes. In particular, fluctuations in temperature affect the fluidity of cytoplasmic and thylakoid membranes. The molecular mechanisms responsible for the perception of changes in membrane fluidity have not been fully characterized. However, the understanding of the functions of the individual genes for fatty acid desaturases in cyanobacteria and plants led to the directed mutagenesis of such genes that altered the membrane fluidity of cytoplasmic and thylakoid membranes. Characterization of the photosynthetic properties of the transformed cyanobacteria and higher plants revealed that lipid unsaturation is essential for protection of the photosynthetic machinery against environmental stresses, such as strong light, salt stress, and high and low temperatures. The unsaturation of fatty acids enhances the repair of the damaged photosystem II complex under stress conditions. In this review, we summarize the knowledge on the mechanisms that regulate membrane fluidity, on putative sensors that perceive changes in membrane fluidity, on genes that are involved in acclimation to new sets of environmental conditions, and on the influence of membrane properties on photosynthetic functions.     

Roles of sulfate adsorption and base cation supply in controlling the chemical response of streams of western Virginia to reduced acid deposition

Micro-organisms are vital for the functioning of all food webs and are the major drivers of the global biogeochemical cycles. The microbial community compositions and physicochemical conditions of the different water masses in the North Sea, a biologically productive sea on the northwestern European continental shelf, were studied during two summer cruises, in order to provide detailed baseline data for this region and examine its microbial biogeography. For each cruise the stations were clustered according to their physicochemical characteristics and their microbial community composition. The largest cluster, which covered most of the central and northern North Sea, consisted of stations that were characterized by a thermally stratified water column and had low chlorophyll a autofluorescence and generally low microbial abundances. The second main cluster contained stations that were dominated by picoeukaryotes and showed the influence of influxes of North Atlantic water via the English Channel and south of the Shetland Islands. The third main cluster was formed by stations that were dominated by cyanobacteria and nanoeukaryotes in the reduced salinity Norwegian Coastal and Skagerrak waters, while the fourth cluster represented the German Bight, a region with strong riverine input, high nutrient concentrations, and consequently high heterotrophic bacterial and viral abundances. Despite the complex and dynamic hydrographic nature of the North Sea, the consistent distinctions in microbiology between these different hydrographic regions during both cruises illustrate the strong links between the microbial community and its environment, as well as the possibility to use microorganisms for long-term monitoring of environmental change.