Gd3+ Encapsulation on 2D-g-C3N4 Nanostructure for Spintronics and Ultrasound Assisted Photocatalytic Applications: First-Principles and Experimental Studies

Atomically thin two-dimensional (2D) semiconductors have high potential in optoelectronics and magneto-optics appliances due to their tunable band structures and physicochemical stability. The work demonstrates that Gd3+ incorporated 2D-g-C3N4 nanosheet (Gd3+/2D-g-C3N4 NS) is synthesized through chemisorption methodology for defect enrichment. The material characterizations reveal that the ion decoration enhances the surface area and defect concentration of the 2D sheet. The experimental observations have been further corroborated with the help of density functional theory (DFT) simulation. Spin asymmetry polarizations near the Fermi level, obtained through the partial density of states (PDOS) analyses, reveal the magnetic nature of the synthesized material, validating the room temperature ferromagnetism obtained through a vibrating-sample magnetometer (VSM). Gd3+/2D-g-C3N4 NS shows significant enhancement in saturation magnetization (Ms) experimentally and computationally compared to the pristine one. The magnetic catalyst shows 98% remediation efficiency for ultrasound-assisted visible-light-driven photodegradation of methyl orange (MO). The synergistic approach of liquid chromatography-mass spectrometry (LC-MS) analyses and DFT studies elucidates reaction intermediates and unveils the degradation mechanism. Post-characterization studies assure the stability of the magnetic catalyst through optical, chemical, magnetic, and microscopic analyses. So, the synthesized material can be proficiently used as a magnetic nanocatalyst in wastewater treatments and spin-electronics applications.

A comprehensive diffusion-induced stress coupled multiscale modeling and analysis in hard-carbon electrodes of Li-ion batteries

Particle fracture due to diffusion-induced stress (DIS) in electrodes is a key factor for lithium-ion battery (LIB) failure. Among many ways to minimize DIS, optimization of particle size and C-rates using state of charge (SOC) dependent varying properties can be a noble approach. Herein, a comprehensive multiscale modeling approach has been proposed to optimize the particle size by studying the DIS in hard carbon (HC) particles as the potential anode materials for high-energy LIBs. To accomplish this, density functional theory (DFT) was used to calculate the SOC dependent coefficient of volume expansion (CVE). Similarly, SOC dependent diffusivity and elastic modulus are calculated via molecular dynamics (MD) simulations. These results are transferred to a continuum model to examine the evolution of concentrations and DISs in hard carbon particles of radius 100-1000 nm lithiated at various C-rates (1C, 2C, 5C, and 10C). Our model successfully incorporates the variation of Li⁺ diffusivity and elastic modulus with SOC and tracks stress relaxation and volume expansion in the particles during lithiation. An optimized particle size has been recommended for hard carbon, considering both stresses for different C-rates. Our study provides a more realistic multiscale modeling framework for optimizing the DIS and can act as a guiding method towards achieving an optimum particle size so that capacity fading due to cracking can be avoided.

Dimensionality effects of g-C3N4 from wettability to solar light assisted self-cleaning and electrocatalytic oxygen evolution reaction

Unique interfacial properties of 2D materials make them more functional than their bulk counterparts in a catalytic application. In the present study, bulk and 2D graphitic carbon nitride nanosheet (bulk g-C₃N₄ and 2D-g-C₃N₄ NS) coated cotton fabrics and nickel foam electrode interfaces have been applied for solar light-driven self-cleaning of methyl orange (MO) dye and electrocatalytic oxygen evolution reaction (OER), respectively. Compared to bulk, 2D-g-C₃N₄ coated interfaces show higher surface roughness (1.094 > 0.803) and enhanced hydrophilicity (θ ∼ 32° < 62° for cotton fabric and θ ∼ 25° < 54° for Ni foam substrate) due to oxygen defect induction as confirmed from morphological (HR-TEM and AFM) and interfacial (XPS) characterizations. The self-remediation efficiencies for blank and bulk/2D-g-C₃N₄ coated cotton fabrics are estimated through colorimetric absorbance and average intensity changes. The self-cleaning efficiency for 2D-g-C₃N₄ NS coated cotton fabric is 87%, whereas the blank and bulk-coated fabric show 31% and 52% efficiency. Liquid Chromatography-Mass Spectrometry (LC-MS) analysis determines the reaction intermediates for MO cleaning. 2D-g-C₃N₄ shows lower overpotential (108 mV) and onset potential (1.30 V) vs. RHE for 10 mA cm^-2 OER current density in 0.1 M KOH. Also, the decreased charge transfer resistance (R_CT = 12 Ω) and lower Tafel's slope (24 mV dec^-1) of 2D-g-C₃N₄ make it the most efficient OER catalyst over bulk-g-C₃N₄ and state-of-the-art material RuO₂. The pseudocapacitance behavior of OER governs the kinetics of electrode-electrolyte interaction through the electrical double layer (EDL) mechanism. The 2D electrocatalyst demonstrates long-term stability (retention ∼94%) and efficacy compared to commercial electrocatalysts.

Lithium and phosphorus-functionalized graphitic carbon nitride monolayer for efficient hydrogen storage: A DFT study

We have explored the consequence of lithium and phosphorous functionalization on the graphitic carbon nitride (g-C₃N₄) monolayer for hydrogen storage using density functional theory. Both pristine and Li and P decorated g-C₃N₄ show a semiconductor nature. The substantial overlap between the s orbital of Li and the p orbital of nitrogen near the Fermi level shows the binding between Li and the g-C₃N₄. The repositioning of HOMO and LUMO is noticed in the Li and P decorated g-C₃N₄. The Bader charge analysis indicates the charge allocation from the Li and P atom to the g-C₃N₄, which results in the adsorption of H₂ by electrostatic interaction. The hydrogen storage capacity of 5.78 wt% is obtained after functionalizing Li and P into the g-C₃N₄. The obtained adsorption energies for the H₂ adsorption and the H₂ desorption temperature confirm that Li and P functionalized g-C₃N₄ is a fascinating candidate for the reversible loading of H₂ at ambient conditions.

A facile and green synthesis of Mn and P functionalized graphitic carbon nitride nanosheets for spintronics devices and enhanced photocatalytic performance under visible-light

Manganese and phosphorus co-doped, graphitic carbon nitride (g-C₃N₄) nanosheet (Mn/P-g-C₃N₄) is prepared by facile and green calcination process of melamine (C₃H₆N₆), manganese chloride tetrahydrate (MnCl₂·4H₂O), and ammonium dihydrogen phosphate ((NH₄)H₂PO₄). The Mn/P co-doping significantly enhances magnetic values compared to pristine-g-C₃N₄, phosphorus-doped g-C₃N₄ (P-g-C₃N₄), and manganese-doped g-C₃N₄ (Mn-g-C₃N₄). We find that Mn/P-g-C₃N₄ is a half-metallic ferromagnetic material having a magnetic moment and Curie temperature of 4.51 μ_B and ∼ 800 K, respectively. The ultraviolet-visible (UV-vis) absorption spectrum of Mn/P-g-C₃N₄ reveals superior absorption in broader wavelength compared to pristine-g-C₃N₄, P-g-C₃N₄, and Mn-g-C₃N₄. The methyl orange degradation efficiency of Mn/P-g-C₃N₄ photocatalyst is 94 %, which is three times more than that of pristine-g-C₃N₄ (29 %) and more significant than the P-g-C₃N₄ (46 %) and Mn-g-C₃N₄ (58 %). Furthermore, density functional theory (DFT) calculation explains the origin of high magnetic behavior, the boosted photocatalytic efficiency of Mn/P-g-C₃N₄, and the essential material properties like structure, bandgap, the density of states (DOS), and atomic level interaction. This work may be helpful for reasonably designing ferromagnetic material for spintronics devices and boosting visible-light (VL) photocatalytic performance for environmental remediation.

Density functional theory-based analyses on selective gas separation by β-PVDF-supported ionic liquid membranes

Finding proper candidates for polymer-supported ionic liquid (IL)-based gas separating membranes is a challenge. The current article elucidates the quantum chemical perspective of the selective gas adsorption efficiency, from a mixture of CO₂, CO, CH₄, and H₂, of α- and β-polyvinylidene fluoride (PVDF)-supported imidazolium- and pyridinium-based six ionic liquid membranes. Although IL-based membrane efficiency mainly depends on the gas solubility of ILs, IL/support binding and gas adsorption on the support material are also studied to describe the overall gas adsorption properties of the PVDF/IL complexes. β-PVDF exhibits better binding with the ILs, and better gas affinity, thus, qualified as a more suitable membrane component as compared to α-PVDF. Dispersion-corrected density functional calculations are performed to provide a detailed insight into the energetic interactions, nonbonding intermolecular interactions based on symmetry adapted perturbation theory (SAPT), natural bond orbitals (NBO), Bader's quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), frontier orbital interactions, density of states (DOS), and thermochemical analyses of the gas-adsorbed systems. Gas molecules interact with the membrane components through weak hydrogen bonds and exhibit low interaction energies, indicating physisorption of the gases. Gas adsorption energies are more negative than the mutual interaction energies of the gas molecules, ensuring effective gas adsorption by the membrane components. All the β-PVDF/IL systems have shown the highest and lowest affinity for CO2 and H2, respectively, leading to effective separation of CO₂ and H₂ from the other gases.

Lanthanum ions decorated 2-dimensional g-C3N4 for ciprofloxacin photodegradation

The low band gap energy and high surface area two-dimensional materials allow it to tune its basic properties using surface decoration. Here, La³⁺ are decorated on two-dimensional graphitic carbon nitride using a simple and easily scalable chemisorption process with an adsorption capacity of 657.32 mg g^-1. In the X-ray diffraction (XRD) study, the positive slope of the W-H plot elucidates the tensile strain generation (0.103) in La³⁺ ions decorated 2D-g-C₃N₄ (La³⁺-2D-g-C₃N₄). The high-resolution transmission electron microscope (HR-TEM) study and the higher I_D/I_G ratio (0.82) in the Raman spectroscopy study confirm the more defects intensification in La³⁺-2D-g-C₃N₄. The reduction in band gap energy for La³⁺-2D-g-C₃N₄ (from 2.83 eV to 2.21 eV) has shown a good correspondence with the band structures study as obtained from the DFT study. In the DFT study, the significant contributions of N atoms in charge transfer validate the N 1s findings from the X-ray photoelectron spectroscopy (XPS) study for La³⁺-2D-g-C₃N₄. La³⁺-2D-g-C₃N₄ shows the photodegradation efficiency (93%) of ciprofloxacin under UV irradiation, which is superior to pristine 2D-g-C₃N₄ (82%) as well as other g-C₃N₄ based nanocatalysts. Also, La³⁺ decoration results in enhancement (32.3%) in photodegradation kinetics rate. The degradation and kinetics studies in the presence of different scavengers ensure that the O₂- and OH^- radicals are mostly responsible for the ciprofloxacin photodegradation. The Liquid chromatographic-mass spectroscopy and the high-performance liquid chromatography studies confirm the photodegradation. The reusability of La³⁺-2D-g-C₃N₄ is tested up to the fifth cycle. FTIR and UV-visible absorption spectroscopy confirm the stability of the used photocatalyst.

Density functional theory based studies on the adsorption of rare-earth ions from hydrated nitrate salt solutions on g-C3N4 monolayer surface

This article represents density functional theory (DFT) based comparative analysis on six trivalent rare-earth ions (RE³⁺; RE: Y, La, Ce, Sm, Eu and Gd) absorption, from the respective nitrate-hexahydrate salts, on graphitic carbon nitride (g-C₃N₄) 2D monolayer, and the photocatalytic properties of the RE³⁺ adsorbed g-C₃N₄ systems (g-C₃N₄/RE³⁺) based on the ground-state electronic structure calculations. Structure, stability and coordination chemistry of two configurations of each hydrated RE-salt system are discussed in detail. Both DFT (B3LYP/SDD) and semi-empirical (Sparkle/PM7) calculations identify the central N₆ vacancy of pristine g-C₃N₄ as the most suitable site for RE³⁺ adsorption. Bader's QTAIM, Mayer bond order and charge population analyses (ADCH, CHELPG and DDEC) are performed to describe the bond characteristics within the systems under study. Thermochemical calculations suggest that the adsorption process is thermodynamically more feasible for higher atomic number (Z) RE³⁺ [Sm³⁺, Eu³⁺ and Gd³⁺], compared to lower-Z RE³⁺ [Y³⁺, La³⁺ and Ce³⁺] ions. Besides, the better photocatalytic properties of higher-Z RE³⁺ adsorbed g-C₃N₄ systems are revealed from better HOMO-LUMO delocalization, decreased HOMO-LUMO gap, increased softness, higher electrophilicity and electron transfer parameter, compared to pristine or lower-Z RE³⁺ adsorbed g-C₃N₄ systems, as obtained from Hirshfeld orbital compositions, density of states and condensed Fukui function analyses.

Nonbonding interaction analyses on PVDF/[BMIM][BF4] complex system in gas and solution phase

The present study provides a detailed quantum chemical description of the physicochemical interactions between poly-vinylidene fluoride (PVDF) and 1-butyl-3-methyl-imidazolium tetrafluoro borate ([BMIM][BF₄]) ionic liquid (IL). Geometry optimization and frequency calculations are carried out for four monomer units of α- and β-PVDF, [BMIM][BF₄], and PVDF/[BMIM][BF₄] using dispersion corrected density functional theory. The effects of solvation on the systems under study are demonstrated for three polar aprotic solvents, namely tetra-hydrofuran (THF), acetone, and n,n-dimethyl formamide (DMF) using the integral equation formalism polarizable continuum model (IEFPCM). Calculated negative solvation free energy values suggest solution phase stability of the systems under study. Binding and interaction energies for β-PVDF/IL are found higher in magnitude than those for α-PVDF/IL. The nonbonding interaction phenomenon of β-PVDF/[BMIM][BF₄] is elucidated on the basis of natural bond orbital (NBO), Bader's quantum theory of atoms in molecules (QTAIM), delocalization indices, Hirshfeld surface, and reduced density gradient (RDG) analyses. Both anions and cations of ionic liquids are found to show weak van der Waals interaction with PVDF molecule but the anion ([BF₄]^-)/PVDF interaction is found to be stronger than cation ([BMIM]⁺)/PVDF interaction. Inter-unit C-H⋯F type hydrogen bonds are found to show improper (causing blue shifts in vibrational frequencies) nature. Frontier molecular orbital analysis is carried out, and different chemical parameters like electronegativity, chemical potential, chemical hardness and softness, and electrophilicity index are calculated using Koopmans' theorem. Thermochemical calculations are also performed, and the variation in different standard thermodynamic parameters with temperature is formulated. Graphical abstract (a) Hirshfeld surface mapped onto electron density and (b) NCI isosurfaces showing inter-unit interactions of β-PVDF/[BMIM][BF₄].

Poisoning, stings and bites in children-- what is new? An experience from a tertiary care hospital in Kolkata

Poisonings, stings and bites continue to be important cause of pediatric morbidity and hospitalization. The toxic product involved in the poisoning varies in different geographical areas and in same area over time. A retrospective study was conducted amongst the children of the age group up to 12 years admitted to a tertiary care hospital in Kolkata from January 2005 to December 2008. Total number of admissions was 17019 and that for accidental poisoning was 451 (2.65%). Kerosene constituted the largest group (54.55%). Mosquito coil and refill liquid were the new additions to the list of poisons and their ingestion was cause for admission of 15 (3.33%) children. The number of admissions due to stings and bites was 108 (0.63% of all admissions) during the above period. Of all the cases, 9 (1.83%) cases of accidental poisoning and 4 (3.7%) cases of stings and bites died.

Profile of pediatric dengue cases from a tertiary care hospital in Kolkata

A study was conducted on the 52 serologically positive cases of dengue, admitted to the Dept. of Paediatrics, R.G. Kar Medical College & Hospital, from an outbreak in Kolkata. The most unusual feature observed in this study was that the rash in some cases was urticarial and intensely pruritic. The shock appeared early in the course of the disease and it was less commonly associated with bleeding (22%). One out of three dengue cases was a severe disease. It was not possible to predict a severe disease from the early symptomatology.

Atomistic simulation studies of magnetite surface structures and adsorption behavior in the presence of molecular and dissociated water and formic acid

Static energy minimization techniques have been used to elucidate the surface structures of magnetite crystals in pure and hydroxylated forms. Adsorption energy values in the presence of molecular water, dissociate water and simple carboxylic group molecule (formic acid) are calculated and we found that the carboxylic group do not adsorb strongly in most of the pure and hydroxylated surfaces in comparison to water. Since the associated calcium minerals are floated from magnetite using fatty acid collector, our calculations corroborate the flotation practice of removing these impurity minerals from magnetite.

Competitive Adsorption on Wollastonite: An Atomistic Simulation Approach

Atomistic simulation techniques are used to simulate surface structure and adsorption behavior of scarcely floatable wollastonite mineral in the presence of molecular and dissociated water, methanoic acid, and methylamine. The latter two additives represent the two widely used collector head-group molecules. The static energy minimization code METADISE was used to perform the simulation to obtain pure surface energy and adsorption energy in the presence of added molecule. The hydroxylation was performed on those surfaces where low-coordinated silicon was made to saturate by bonding with hydroxyl group, and the subsequent charge neutralization was maintained by adding proton on single-coordinated surface oxygen. A comparison of surface energies revealed that all the surfaces become stabilized in the presence of added molecules; however, the presence of methylamine decreased the surface energy to lower values. Adsorption of dissociated water is preferred by the {100} and {102} surfaces, whereas the {001} surface preferred methylamine adsorption, because these show highly negative adsorption energies. In terms of molecular adsorption, the preferred adsorption sequence for all the surfaces is methylamine > methanoic acid > water without considering coadsorption. For the {100} and {102} surfaces, the adsorption energy values of carboxylic acid and amine are more negative than that of water and therefore we conclude that both carboxyl and amine head-group molecules adsorb preferably on wollastonite. Our simulation verify usability of carboxylic acid head group as widely used collectors for wollastonite flotation and, at the same time, it predicts the use of amine head-group collectors as possible modifiers, which corresponds well with our experimental findings.

Synthesis and unusual electron paramagnetic resonance spectrum of metastable nanoclusters of ZnO semiconductor crystallites

Metastable nanoclusters of ZnO semiconductor crystallites, 20 to 30 nm diameter, are synthesized by a reconstructive decomposition of a polymer precursor of dispersed Zn2+ cations in poly vinyl alcohol (PVA) polymer molecules. They have EPR (electron paramagnetic resonance) spectrum of distinct excitonic features. Multiple EPR bands appear in prominent intensities in oxygen vacancies VO+ and singly ionized Oi- and Zn(i)+ interstitials. A paramagnetic VO+ vacancy derives from usual diamagnetic O2- vacancy of VO++ (behaves as if doubly charged compared to the lattice) by addition of one electron. The results demonstrate the existence of a surface-interface or surface barrier layer in free-carrier depletion at the crystallite surface in the clusters and its effects on the Oi- and Zn(i)+ ionization states (determine green photoluminescence). Both VO+ and Zn(i)+ are curable by a thermal annealing in O2 gas. A cured sample of equilibrium structure achieved by heating at approximately 550 degrees C has a single EPR in Oi- at g = 1.990. The results are useful in understanding their correlation with EPR and optical properties in ZnO semiconductors and devices.

Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo

GCN5 is a histone acetyltransferase (HAT) originally identified in Saccharomyces cerevisiae and required for transcription of specific genes within chromatin as part of the SAGA (SPT-ADA-GCN5 acetylase) coactivator complex. Mammalian cells have two distinct GCN5 homologs (PCAF and GCN5L) that have been found in three different SAGA-like complexes (PCAF complex, TFTC [TATA-binding-protein-free TAF(II)-containing complex], and STAGA [SPT3-TAF(II)31-GCN5L acetylase]). The composition and roles of these mammalian HAT complexes are still poorly characterized. Here, we present the purification and characterization of the human STAGA complex. We show that STAGA contains homologs of most yeast SAGA components, including two novel human proteins with histone-like folds and sequence relationships to yeast SPT7 and ADA1. Furthermore, we demonstrate that STAGA has acetyl coenzyme A-dependent transcriptional coactivator functions from a chromatin-assembled template in vitro and associates in HeLa cells with spliceosome-associated protein 130 (SAP130) and DDB1, two structurally related proteins. SAP130 is a component of the splicing factor SF3b that associates with U2 snRNP and is recruited to prespliceosomal complexes. DDB1 (p127) is a UV-damaged-DNA-binding protein that is involved, as part of a complex with DDB2 (p48), in nucleotide excision repair and the hereditary disease xeroderma pigmentosum. Our results thus suggest cellular roles of STAGA in chromatin modification, transcription, and transcription-coupled processes through direct physical interactions with sequence-specific transcription activators and with components of the splicing and DNA repair machineries.

p300-mediated acetylation of human transcriptional coactivator PC4 is inhibited by phosphorylation

The human positive coactivator 4 (PC4) acts as a general coactivator for activator-dependent transcription, the activity of which is regulated negatively by phosphorylation. We report here that PC4 can be acetylated specifically by another coactivator, p300. Interestingly, phosphorylation of PC4 by casein kinase II inhibits the p300-mediated acetylation. Mass spectral analysis revealed that there are at least two lysine residues acetylated in PC4, as a result of which its DNA binding activity is stimulated.

Activator-dependent transcription from chromatin in vitro involving targeted histone acetylation by p300

The transcriptional coactivator p300 shows physical and functional interactions with a diverse group of activators and contains an intrinsic acetyltransferase activity whose exact coactivator functions in the acetylation of nucleosomal histones versus other factors are poorly documented. Here, we show that p300 mediates acetyl-CoA-dependent transcription by GAL4-VP16 from a nucleosomal array template, that this involves p300 targeting by GAL4-VP16 and promoter-proximal histone acetylation prior to transcription, and that the affinities of different activators for p300 roughly correlate with corresponding levels of p300-dependent transcription. These results indicate that activators recruit p300 to nucleosomal templates by direct interactions and that bound p300 stimulates transcription, at least in part, by localized histone acetylation.

HATs off: selective synthetic inhibitors of the histone acetyltransferases p300 and PCAF

Histone acetyltransferases (HATs) play important roles in the regulation of gene expression. In this report, we describe the design, synthesis, and application of peptide CoA conjugates as selective HAT inhibitors for the transcriptional coactivators p300 and PCAF. Two inhibitors (Lys-CoA for p300 and H3-CoA-20 for PCAF) were found to be potent (IC(50) approximately = 0.5 microM) and selective (approximately 200-fold) in blocking p300 and PCAF HAT activities. These inhibitors were used to probe enzymatic and transcriptional features of HAT function in several assay systems. These compounds should be broadly useful as biological tools for evaluating the roles of HATs in transcriptional studies and may serve as lead agents for the development of novel antineoplastic therapeutics.

The TFIIIC90 subunit of TFIIIC interacts with multiple components of the RNA polymerase III machinery and contains a histone-specific acetyltransferase activity

Human transcription factor IIIC (hTFIIIC) is a multisubunit complex that directly recognizes promoter elements and recruits TFIIIB and RNA polymerase III. Here we describe the cDNA cloning and characterization of the 90-kDa subunit (hTFIIIC90) that is present within a DNA-binding subcomplex (TFIIIC2) of TFIIIC. hTFIIIC90 has no specific homology to any of the known yeast TFIIIC subunits. Immunodepletion and immunoprecipitation studies indicate that hTFIIIC90 is a bona fide subunit of TFIIIC2 and absolutely required for RNA polymerase III transcription. hTFIIIC90 shows interactions with the hTFIIIC220, hTFIIIC110, and hTFIIIC63 subunits of TFIIIC, the hTFIIIB90 subunit of TFIIIB, and the human RPC39 (hRPC39) and hRPC62 subunits of an initiation-specific subcomplex of RNA polymerase III. These interactions may facilitate both TFIIIB and RNA polymerase III recruitment to the preinitiation complex by TFIIIC. We show that hTFIIIC90 has an intrinsic histone acetyltransferase activity with a substrate specificity for histone H3.

CpG islands in chromatin organization and gene expression

CpG islands are stretches of DNA sequence that are enriched in the (CpG)n repeat and are present in close association with all housekeeping genes as well as some tissue-specific genes in the mammalian genome. Methylation of CpG islands strongly influences both structural organization and function of chromatin. The presence of a CpG island in a given chromosomal domain can, by itself, give rise to relatively open and active chromatin. Recently, several histone acetyltransferases, histone deacetylases, and chromatin remodeling factors have been found to be part of the transcription machinery. It is becoming increasingly clear that CpG islands and their methylation status may influence the function or recruitment of these newly discovered chromatin remodeling factors, especially the histone deacetylases. In addition, CpG islands may also play a significant role in the reorganization of chromatin during mammalian spermiogenesis.

Human TFIIIC relieves chromatin-mediated repression of RNA polymerase III transcription and contains an intrinsic histone acetyltransferase activity

Human TFIIIC is a multisubunit factor that is essential for transcription by RNA polymerase III on tRNA and virus-associated RNA genes and initiates preinitiation complex assembly by direct recognition of promoter elements. We show that highly purified TFIIIC, at concentrations above those sufficient for transcription of naked DNA templates, effectively relieves nucleosome-mediated repression on an in vitro-reconstituted chromatin template. Highly purified TFIIIC alone can bind to the A and B boxes of a tRNA gene within a chromatin template and, further, displays a histone acetyltransferase activity that is intrinsic to at least one (and probably three) of its subunits. The possibility of a direct link between TFIIIC-dependent chromatin transcription and acetyltransferase activities is suggested by the partial loss of these activities, but not DNA transcription activity, following pretreatment of TFIIIC with p-hydroxymercuribenzoic acid.

A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID

In yeast, SPT3 is a component of the multiprotein SPT-ADA-GCN5 acetyltransferase (SAGA) complex that integrates proteins with transcription coactivator/adaptor functions (ADAs and GCN5), histone acetyltransferase activity (GCN5), and core promoter-selective functions (SPTs) involving interactions with the TATA-binding protein (TBP). In particular, yeast SPT3 has been shown to interact directly with TBP. Here we report the molecular cloning of a cDNA encoding a human homologue of yeast SPT3. Amino acid sequence comparisons between human SPT3 (hSPT3) and its counterparts in different yeast species reveal three highly conserved domains, with the most conserved 92-amino acid N-terminal domain being 25% identical with human TAFII18. Despite the significant sequence similarity with TAFII18, native hSPT3 is not a bona fide TAFII because it is not associated in vivo either with human TBP/TFIID or with a TFIID-related TBP-free TAFII complex. However, we present evidence that hSPT3 is associated in vivo with TAFII31 and the recently described longer form of human GCN5 (hGCN5-L) in a novel human complex that has histone acetyltransferase activity. We propose that the human SPT3-TAFII31-GCN5-L acetyltransferase (STAGA) complex is a likely homologue of the yeast SAGA complex.

Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes

The rpoF gene of Escherichia coli codes for the RNA polymerase sigmaF (or sigma28) subunit, which is involved in transcription of the flagellar and chemotaxis genes. Both sigmaF and sigma70 (the major sigma subunit in growing cells) were overexpressed, purified to homogeneity, and compared with respect to activity and specificity. The affinity of sigmaF to core RNA polymerase (E) is higher than that of sigma70, as measured by gel filtration high-pressure liquid chromatography. In an in vitro transcription system, the holoenzyme (E sigmaF) containing sigmaF selectively transcribed the flagellar and chemotaxis genes, all of which could not be transcribed by E sigma70. This strict promoter recognition property of sigmaF is similar to those of other stress response minor sigma subunits but different from those of the principal sigma subunits, sigma70 and sigma38. sigma70-dependent transcription in vitro is inhibited at high concentrations of all salts tested, showing maximum activity at 50 mM. In contrast, sigmaF-dependent transcription was maximum at 50 mM KCI and then decreased to negligible level at 300 mM; in the cases of potassium acetate and potassium glutamate, maximum transcription was between 200 and 300 mM. DNase I foot printing of the fliC and fliD promoters indicated that sigmaF alone is unable to bind DNA, but E sigmaF specifically recognizes -10 and -35 regions of the sigmaF-dependent promoters with rather long upstream protection. Alteration of the promoter structure after binding of E sigmaF was suggested.

Zinc dependent recognition of a human CpG island sequence by the mammalian spermatidal protein TP2

Rat spermatidal protein TP2 is a zinc metalloprotein with two atoms of zinc coordinated to cysteine and histidine residues and condenses alternating GC copolymer preferentially in a zinc dependent manner [Kundu, T. K., & Rao, M. R. S. (1995) Biochemistry 34,5143-5150]. In the present study, we have used a 40-mer oligonucleotide containing a human CpG island sequence to study its interaction with TP2 by gel mobility shift assays. A specific complex was observed in the presence of poly(dI).poly(dC). Preincubation of TP2 with 10 mM EDTA or 1 mM 1, 10-o-phenanthroline inhibited the complex formation by more than 90%. Competition experiments with various polynucleotides revealed the following order of efficiency: poly(dG-dC).poly(dG-dC) > cold homologous oligonucleotide > poly(dA-dT).poly(dA-dT). Homoduplexes poly(dG).poly(dC) and poly(dA).poly(dT) had no effect on the complex formation. Chromomycin A3, a GC minor groove binding drug, inhibited the complex formation. Methylation of the CpG doublet within the CpG island sequence by SssI methylase (CpG methylase) completely abolished the complex formation. Methylation of G at the N-7 position with dimethyl sulfate did not affect the recognition of CpG island by TP2. Thus, CpG islands, widely distributed in the mammalian genome, may serve as specific loci for initiation of chromatin condensation by TP2 during the later stages of spermiogenesis.

A method for in vivo [32P]phosphate labelling of testis proteins

The direct intratesticular injection of [32P]phosphate resulted in 4-9 times more labelling of rat testis proteins compared to the conventional method of in vitro incubation. Moreover this is a simple technique requiring minimum (7-10 times less) radioactive phosphate and is less hazardous.

DNA condensation by the rat spermatidal protein TP2 shows GC-rich sequence preference and is zinc dependent

Transition protein-2 (TP2), isolated from rat testes, was recently shown to be a zinc metalloprotein. We have now carried out a detailed analysis of the DNA condensing properties of TP2 with various polynucleotides using circular dichroism spectroscopy. The condensation of the alternating copolymers by TP2 (incubated with 10 microM ZnSO4), namely, poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT), was severalfold higher than condensation of either of the homoduplexes poly(dG).poly-(dC) and poly(dA).poly(dT) or rat oligonucleosomal DNA. Between the two alternating copolymers, poly(dG-dC).poly(dG-dC) was condensed 3.2-fold more effectively than poly(dA-dT).poly(dA-dT). Preincubation of TP2 with 5 mM EDTA significantly reduced its DNA-condensing property. Interestingly, condensation of the alternating copolymer poly(dI-dC).poly(dI-dC) by TP2 was much less as compared to that of poly(dG-dC).poly(dG-dC). The V8 protease-derived N-terminal fragment (88 aa) condensed poly(dA-dT).poly(dA-dT) to a very small extent but did not have any effect on poly(dG-dC).poly-(dG-dC). The C-terminal fragment (28 aa) was able to condense poly(dA-dT).poly(dA-dT) more effectively than poly(dG-dC).poly(dG-dC). These results suggest that TP2 in its zinc-coordinated form condenses GC-rich polynucleotides much more effectively than other types of polynucleotides. Neither the N-terminal two-thirds of TP2 which is the zinc-binding domain nor the C-terminal basic domain are as effective as intact TP2 in bringing about condensation of DNA.

Characterization of the zinc-metalloprotein nature of rat spermatidal protein TP2

Spermatidal transition protein, TP2, was purified from rat testes by Hg-affinity chromatography. The present study reports the details of the zinc-metalloprotein nature of TP2 by employing the 65 Zn-blotting technique. Chemical modification of cysteine by iodoacetic acid, and histidine by diethylpyrocarbonate, resulted in a near complete inhibition of 65Zn-binding to TP2. The 65Zinc-binding was localized to the V8 protease-derived N-terminal two-third polypeptide fragment. Circular dichroism spectroscopy studies of TP2 (zinc pre-incubated) and its V8 protease-derived polypeptide fragments revealed that the N-terminal fragment has a Type I-beta-turn spectrum, while the C-terminal fragment has a small but significant alpha-helical structure. EDTA altered the circular dichroism spectrum of TP2 and the N-terminal fragment (zinc binding domain) but not that of the C-terminal fragment.