Interdomain and membrane interactions of CTP:phosphocholine cytidylyltransferase revealed via limited proteolysis and mass spectrometry

CTP:phosphocholine cytidylyltransferase (CCT) is a multi-domain enzyme that regulates phosphatidylcholine synthesis. It converts to an active form upon binding cell membranes, and interdomain dissociations have been hypothesized to accompany this process. To identify these interdomain and membrane interactions, the tertiary structures of three forms of CCTalpha were probed by monitoring accessibility to proteases. Time-limited digestion with chymotrypsin or arginine C of soluble CCTalpha (CCT(sol)), phospholipid vesicle-bound CCT (CCT(mem)), and a soluble constitutively active CCT truncated at amino acid 236 generated complex mixtures of peptides that were resolved and identified by gel electrophoresis/immunoblotting and by matrix-assisted laser desorption/ionization-mass spectrometry, with or without coupling to capillary liquid chromatography. Identification of cleavage sites enabled assembly of peptide bond accessibility maps for each CCT form. Our results reveal a approximately 80-residue core within the catalytic domain (domain C) as the most inaccessible region in all three forms and the C-terminal phosphorylation domain as the most accessible. Membrane binding has little effect on the protease accessibility of these domains. To map the protease sites onto the catalytic domain, its three-dimensional structure was modeled from the atomic coordinates of glycerol-phosphate cytidylyltransferase (Protein Data Bank code 1COZ). The protease inaccessibility of most sites in domain C could be explained by burial or location within secondary structural elements. The accessibility of the N-terminal domain (domain N) was enhanced upon membrane binding. Residues Phe(234)-Leu(303) were inaccessible in CCT(mem), suggesting burial in the membrane. Surprisingly, residues Leu(274)-Leu(303) of this domain were also inaccessible in CCT(sol). We propose that this region is buried by interdomain contacts with domain N in CCT(sol). Membrane binding and burial of domain M in the lipid bilayer may disrupt this interaction, leading to increased exposure of sites in domain N.     

Pulmonary function and fuel use: A population survey

Background

In the backdrop of conflicting reports (some studies reported adverse outcomes of biomass fuel use whereas few studies reported absence of any association between adverse health effect and fuel use, may be due to presence of large number of confounding variables) on the respiratory health effects of biomass fuel use, this cross sectional survey was undertaken to understand the role of fuel use on pulmonary function.

Method

This study was conducted in a village of western India involving 369 randomly selected adult subjects (165 male and 204 female). All the subjects were interviewed and were subjected to pulmonary function test. Analysis of covariance was performed to compare the levels of different pulmonary function test parameters in relation to different fuel use taking care of the role of possible confounding factors.

Results

This study showed that biomass fuel use (especially wood) is an important factor for deterioration of pulmonary function (particularly in female). FEV₁ (p < .05), FEV₁ % (p < .01), PEFR (p < .05) and FEF_25–75 (p < .01) values were significantly lower in biomass fuel using females than nonusers. Comparison of only biomass fuel use vs. only LPG (Liquefied Petroleum Gas) use and only wood vs. only LPG use has showed that LPG is a safer fuel so far as deterioration of pulmonary function is concerned. This study observes some deterioration of pulmonary function in the male subjects also, who came from biomass fuel using families.

Conclusion

This study concluded that traditional biomass fuels like wood have adverse effects on pulmonary function.     

Use of infrared spectroscopy to monitor protein structure and stability

One of the most versatile methods for monitoring the structure of proteins, either in solution or in the solid state, is Fourier transform infrared spectroscopy. Also known as mid-range infrared, which covers the frequency range from 4000 to 400 cm(-1), this wavelength region includes bands that arise from three conformationally sensitive vibrations within the peptide backbone (amide I, II and III). Of these vibrations, amide I is the most widely used and can provide information on secondary structure composition and structural stability. One of the advantages of infrared spectroscopy is that it can be used with proteins that are either in solution or in the solid state. The use of infrared to monitor protein structure and stability is summarized herein. In addition, specialized infrared methods are presented, such as techniques for the study of membrane proteins and oriented samples. In addition, there is a growing body of literature on the use of infrared to follow reaction kinetics and ligand binding in proteins, as well as a number of infrared studies on protein dynamics. Finally, the potential for using near-infrared spectroscopy to study protein structure is introduced.     

CTP:phosphocholine cytidylyltransferase and protein kinase C recognize different physical features of membranes: differential responses to an oxidized phosphatidylcholine

Protein kinase C (PKC) and CTP:phosphocholine cytidylyltransferase (CT) are two examples of enzymes that are regulated by reversible binding to membranes, and this binding is influenced by membrane physical properties. CT activation by oxidized phosphatidylcholines was recently demonstrated and was linked to the acyl chain disordering effect of the oxidized species (Biochemistry 38, 15606). In this paper, we compare the responses of PKC and CT to an oxidized PC, and investigate the physical properties of lipid bilayers that modulate the activity of these enzymes. We show that 1-palmitoyl, 2-(11,15 dihydroxy) eicosatrienoyl PC (diOH-PAPC) caused less of an increase in the temperature of the lamellar to hexagonal II transition (T(H)) of an unsaturated PE, compared to its parent, PAPC. Using a polarity-sensitive interfacial probe, we also found evidence to suggest that this oxidized PC increases interfacial packing pressure. We found that whereas diOH-PAPC activates CT, it inhibits PKC relative to the parent PAPC. The activities of both CT and PKC are known to increase in the presence of non-lamellar forming lipids. The greater activating effect of diOH-PAPC compared with PAPC, is consistent with a stimulation of the activity of CT by negative curvature strain. However, this is not the case with PKC, for which we suggest that surface packing pressure is of prime importance.     

Regulation of CTP: phosphocholine cytidylyltransferase activity by the physical properties of lipid membranes: an important role for stored curvature strain energy

CTP:Phosphocholine cytidylyltransferase (CT) catalyzes the key step in phosphatidylcholine (PC) synthesis. CT is activated by binding to certain lipid membranes. The membrane binding affinity of CT can vary from micromolar to millimolar K(d), depending on the lipid composition of the target membrane. Class II CT activators like diacylglycerols and unsaturated phosphatidylethanolamines (PE) favor inverted lipid phase formation. The mechanism(s) governing CT's association with class II lipid membranes and subsequent activation are relatively unknown. We measured CT activation by vesicles composed of PC and one of three unsaturated PEs, dioleoylglycerol (DOG), or cholesterol. For each lipid system, we estimated the stored curvature strain energy of the monolayer when confined to a relatively flat bilayer. CT binding and activation correlate very well with the curvature strain energy of several chemically distinct class II lipid systems, with the exception of those containing cholesterol, in which CT activation was less than the increase in curvature strain. CT activation by membranes containing DOG was reversed by inclusion of specific lysolipids, which reduce curvature strain energy. LysoPC, which has a larger positive curvature than lysoPE, produced greater inhibition of CT activation. Stored curvature strain energy is thus an important determinant of CT activation. Membrane interfacial polarity was investigated using a membrane-anchored fluorescent probe. Decreases in quenching of this interfacial probe by doxyl-PCs in class II membranes suggest the probe adopts a more superficial membrane location. This may reflect an increased surface hydrophobicity of class II lipid membranes, implying a role for surface dehydration in CT's interactions with membranes containing class II lipids. Cholesterol, a poor activator of CT, did not affect the positioning of the polarity-sensitive probe, suggesting that one reason for its ineffectiveness is an inability to enhance surface hydrophobicity.     

Coral species richness: ecological versus biogeographical influences

Species richness in communities varies with habitat area, productivity, disturbance level, intensity of species interactions, and regional/historical effects. All of these factors influence coral richness but their effects vary with spatial scale, position on the reef, and regional location. Species richness of corals along depth gradients shows a unimodal, hump-shaped curve that peaks at intermediate depths. Moreover, the peak of the curve is higher in regions with larger species pools. This “regional enrichment” of the local community appears in line transect samples as small as 10 m in length. The pattern suggests that ecological factors operating over scales of tens of meters and regional/historical factors operating over thousands of kilometers can both affect local richness. Regional factors probably include differences in speciation relative to extinction rates among regions and proximity of local sites to richness hotspots. Plausible factors operating at the local scale are species interactions, disturbance, and productivity which combine in different ways to produce the unimodal pattern. Shallow areas support few species because extinction rates are high due to frequent disturbance or because of environmental extremes. In addition, high productivity encourages rapid growth and thus the potential for intense interspecific competition. In areas where branching acroporids are abundant, exclusion by these dominant competitors is possible. Deep areas may be depauperate because few species can tolerate the low light levels found there. Areas of intermediate depth have the richest communities because they are open for colonization by many species and because extinction rates are low. Several theories may explain this “openness” and species persistence: 1. Occasional disturbance coupled with low growth rates results in glacially slow exclusion by the dominant competitor. 2. Aggregation of corals creates spatial variation in the intensity of competition and thus refuges from competition within a spatial landscape. Inferior competitors persist because they are superior at dispersal and refuge colonization. 3. Specialist predators focus on high-density juvenile populations near the parent, creating ecological space for colonization by non-prey. 4. Coral competitive abilities are roughly equal and recruitment into the community is a probabilistic event. The community thus exhibits random drift and exclusion is an extremely lengthy process. Based upon empirical evidence, these theories are listed in order of plausibility, but still need to be rigorously tested. Accepted: 9 September 1999     

Solubilization and reconstitution of cholinephosphotransferase from sarcoplasmic reticulum: stabilization of solubilized enzyme by diacylglycerol and glycerol

Cholinephosphotransferase (CDPcholine: 1,2-diacylglycerol cholinephosphotransferase, EC 2.7.8.2), which catalyzes the terminal step in phosphatidylcholine synthesis via the CDPcholine pathway, is present in sarcoplasmic reticulum from rabbit skeletal muscle (Cornell, R. and MacLennan, D.H. (1985) Biochim. Biophys. Acta 835, 567-576). The conditions for solubilization and reconstitution of this enzyme were investigated as a preliminary step towards its eventual purification. The activity was not released by treatment of membranes with 1 M KCl, but was solubilized after dissolution of membranes with detergents. Cholinephosphotransferase was inactivated by cholate, deoxycholate, Triton X-100, octylglucoside, Tween-20 or SDS at concentrations which solubilize the membrane. However, the activity could be fully recovered after reconstituting the membrane by adding excess lipid (soybean) and removing detergent by gel filtration, dialysis or by absorption to Bio-Beads. When the membrane was solubilized with octylglucoside or cholate at weight ratios of detergent: membrane protein of at least 10, the activity was irreversibly lost unless stabilizers were added with detergent. The substrate diacylglycerol and glycerol were effective stabilizers.     

Virus genome dynamics under different propagation pressures: reconstruction of whole genome haplotypes of west nile viruses from NGS data

Background

Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies population variants. These variants are not discernable in the consensus genome at the time of emergence, and the maintenance of mutation-selection equilibria of population variants is greatly underestimated. The emergence of lineage 1 WNV strains has been studied extensively, but recent epidemics caused by lineage 2 WNV strains in Hungary, Austria, Greece and Italy emphasizes the increasing importance of this lineage to public health. In this study we explored the quasispecies dynamics of minority variants that contribute to cell-tropism and host determination, i.e. the ability to infect different cell types or cells from different species from Next Generation Sequencing (NGS) data of a historic lineage 2 WNV strain.

Results

Minority variants contributing to host cell membrane association persist in the viral population without contributing to the genetic change in the consensus genome. Minority variants are shown to maintain a stable mutation-selection equilibrium under positive selection, particularly in the capsid gene region.

Conclusions

This study is the first to infer positive selection and the persistence of WNV haplotype variants that contribute to viral fitness without accompanying genetic change in the consensus genotype, documented solely from NGS sequence data. The approach used in this study streamlines the experimental design seeking viral minority variants accurately from NGS data whilst minimizing the influence of associated sequence error.     

Coxsackievirus B Exits the Host Cell in Shed Microvesicles Displaying Autophagosomal Markers

Coxsackievirus B3 (CVB3), a member of the picornavirus family and enterovirus genus, causes viral myocarditis, aseptic meningitis, and pancreatitis in humans. We genetically engineered a unique molecular marker, “fluorescent timer” protein, within our infectious CVB3 clone and isolated a high-titer recombinant viral stock (Timer-CVB3) following transfection in HeLa cells. “Fluorescent timer” protein undergoes slow conversion of fluorescence from green to red over time, and Timer-CVB3 can be utilized to track virus infection and dissemination in real time. Upon infection with Timer-CVB3, HeLa cells, neural progenitor and stem cells (NPSCs), and C2C12 myoblast cells slowly changed fluorescence from green to red over 72 hours as determined by fluorescence microscopy or flow cytometric analysis. The conversion of “fluorescent timer” protein in HeLa cells infected with Timer-CVB3 could be interrupted by fixation, suggesting that the fluorophore was stabilized by formaldehyde cross-linking reactions. Induction of a type I interferon response or ribavirin treatment reduced the progression of cell-to-cell virus spread in HeLa cells or NPSCs infected with Timer-CVB3. Time lapse photography of partially differentiated NPSCs infected with Timer-CVB3 revealed substantial intracellular membrane remodeling and the assembly of discrete virus replication organelles which changed fluorescence color in an asynchronous fashion within the cell. “Fluorescent timer” protein colocalized closely with viral 3A protein within virus replication organelles. Intriguingly, infection of partially differentiated NPSCs or C2C12 myoblast cells induced the release of abundant extracellular microvesicles (EMVs) containing matured “fluorescent timer” protein and infectious virus representing a novel route of virus dissemination. CVB3 virions were readily observed within purified EMVs by transmission electron microscopy, and infectious virus was identified within low-density isopycnic iodixanol gradient fractions consistent with membrane association. The preferential detection of the lipidated form of LC3 protein (LC3 II) in released EMVs harboring infectious virus suggests that the autophagy pathway plays a crucial role in microvesicle shedding and virus release, similar to a process previously described as autophagosome-mediated exit without lysis (AWOL) observed during poliovirus replication. Through the use of this novel recombinant virus which provides more dynamic information from static fluorescent images, we hope to gain a better understanding of CVB3 tropism, intracellular membrane reorganization, and virus-associated microvesicle dissemination within the host.