Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase

CFE88 is a conserved essential gene product from Streptococcus pneumoniae. This 227-residue protein has minimal sequence similarity to proteins of known 3D structure. Sequence alignment models and computational protein threading studies suggest that CFE88 is a methyltransferase. Characterization of the conformation and function of CFE88 has been performed by using several techniques. Backbone atom and limited side-chain atom NMR resonance assignments have been obtained. The data indicate that CFE88 has two domains: an N-terminal domain with 163 residues and a C-terminal domain with 64 residues. The C-terminal domain is primarily helical, while the N-terminal domain has a mixed helical/extended (Rossmann) fold. By aligning the experimentally observed elements of secondary structure, an initial unrefined model of CFE88 has been constructed based on the X-ray structure of ErmC' methyltransferase (Protein Data Bank entry 1QAN). NMR and biophysical studies demonstrate binding of S-adenosyl-L-homocysteine (SAH) to CFE88; these interactions have been localized by NMR to the predicted active site in the N-terminal domain. Mutants that target this predicted active site (H26W, E46R, and E46W) have been constructed and characterized. Overall, our results both indicate that CFE88 is a methyltransferase and further suggest that the methyltransferase activity is essential for bacterial survival.     

The iron chelator desferrioxamine inhibits atherosclerotic lesion development and decreases lesion iron concentrations in the cholesterol-fed rabbit

Several epidemiological studies have suggested that increased iron stores are associated with increased atherosclerotic events. In order to test the hypothesis that decreasing the vascular level of iron slows lesion growth, we examined the effects of the iron chelator Desferal (72 mg/kg/day, 5 days/week) on atherosclerosis and lesion iron content in cholesterol-fed New Zealand White rabbits. Rabbits were fed with a 1% w/w cholesterol diet for either 8 weeks (and for the last 5 weeks injected daily with Desferal) or 12 weeks (and for the last 9 weeks injected with Desferal). Controls were injected with saline. A significant reduction in average lesion area (p = 0.038) was observed in the 12-week treated animals compared with the 12-week controls. The average lesion iron level of the 12-week treated animals (58 ppm dry wt) was also significantly lower (p = 0.030) than in 12-week control animals (95 ppm dry wt), as measured using nuclear microscopy with the combination of scanning transmission ion microscopy, Rutherford back-scattering spectroscopy, and particle-induced X-ray emission. No reduction in lesion area or iron content was observed in the 8-week treated animals compared with controls, and no change in lesion zinc concentration was observed for either group. Our data strengthen the concept that iron contributes to the early stages of the development of atherosclerosis.     

Adhesion dynamics, morphology, and organization of 3T3 fibroblast on chitosan and its derivative: the effect of O-carboxymethylation

Chitosan and O-carboxymethylchitosan (OCMCS) have been proved to have biocompatibility and have been extensively researched in the field of biomaterials. In this study, Confocal-reflectance interference contrast microscopy (C-RICM) in conjunction with phase contrast imaging was used to investigate the adhesion contact dynamics of 3T3 fibroblasts on chitoan and OCMCS surface-modified silica coverslips. The C-RICM results demonstrate that the weak cell contact forms on OCMCS surface while a much stronger contact area forms on the chitosan surface. 3T3 fibroblasts are found to spread randomly with spindlelike morphology on the chitosan surface, while they exhibit elongated morphology and align on the OCMCS surface. It is believed that fibroblast behaviors such as migration, spreading with an elongated morphology, and alignment on the OCMCS surface are correlated with the weak cell contact. The mechanisms to form cell adhesion contact on chitosan and OCMCS were discussed.     

NF-kappaB and not the MAPK signaling pathway regulates GADD45beta expression during acute inflammation

The GADD45 (growth arrest and DNA damage-inducible) family of genes is involved in the regulation of cell cycle progression and apoptosis. To study signaling pathways affecting GADD45beta expression and to examine systematically in vivo the GADD45beta expression in tissues following various toxic stresses, we created a transgenic mouse by fusing the GADD45beta promoter to firefly luciferase (Gadd45beta-luc). In vivo GADD45beta expression was assessed by measuring the luciferase activity in the Gadd45beta-luc transgenic mouse using a non-invasive imaging system (IVIS Imaging System, Xenogen Corporation). We found that a number of agents that induce oxidative stress, such as sodium arsenite, CCl4, lipopolysaccharide (LPS), or tumor necrosis factor-alpha, are able to induce luciferase expression throughout the entire animal. In liver, spleen, lung, intestine, kidney, and heart, we observed an induction of luciferase activity after LPS treatment, which correlates with an increase of GADD45beta mRNA in these tissues. Processes that induce DNA damage activate the NF-kappaB signaling pathway. Several inhibitors of the NF-kappaB signaling pathway, including dexamethasone, thalidomide, and a proteasome inhibitor, bortezomib, showed inhibitory effects on LPS-induced GADD45beta expression as indicated by a decrease of the luciferase activity. Northern blot analysis confirmed a broad inhibitory effect of bortezomib on LPS-induced GADD45beta mRNA expression in spleen, lung, and intestine. In liver of bortezomib-treated mice, we observed a reverse correlation between the luciferase activity and the GADD45beta mRNA level. We speculate that such a discrepancy could be due to severe liver toxicity caused by bortezomib and LPS co-treatment. MAPK inhibitors had transient and inconsistent effects on LPS-induced luciferase expression. Our data are consistent with the notion that NF-kappaB, but not the MAPK signaling pathways, is involved in the in vivo regulation of GADD45beta expression. Thus, NF-kappaB signaling involves induction of GADD45beta expression, which supports the proposed role of GADD45beta in protecting cells against DNA damaged under various stress conditions.     

Structures of the MthK RCK domain and the effect of Ca2+ on gating ring stability

MthK is a Ca2+-gated K+ channel from Methanobacterium autotrophicum. The crystal structure of the MthK channel in a Ca2+-bound open state was previously determined at 3.3 A and revealed an octameric gating ring composed of eight intracellular ligand-binding RCK (regulate the conductance of K+) domains. It was suggested that Ca2+ binding regulates the gating ring conformation, which in turn leads to the opening and closing of the channel. However, at 3.3 AA resolution, the molecular details of the structure are not well defined, and many of the conclusions drawn from that structure were hypothetical. Here we have presented high resolution structures of the MthK RCK domain with and without Ca2+ bound from three different crystals. These structures revealed a dimeric architecture of the RCK domain and allowed us to visualize the Ca2+ binding and protein-protein contacts at atomic detail. The dimerization of RCK domains is also conserved in other RCK-regulated K+ channels and transporters, suggesting that the RCK dimer serves as a basic unit in the gating ring assembly. A comparison of these dimer structures confirmed that the dimer interface is indeed flexible as suggested previously. However, the conformational change at the flexible interface is of an extent smaller than the previously hypothesized gating ring movement, and a reconstruction of these dimers into octamers by applying protein-protein contacts at the fixed interface did not generate enclosed gating rings. This indicated that there is a high probability that the previously defined fixed interface may not be fixed during channel gating. In addition to the structural studies, we have also carried out biochemical analyses and have shown that near physiological pH, isolated RCK domains form a stable octamer in solution, supporting the notion that the formation of octameric gating ring is a functionally relevant event in MthK gating. Additionally, our stability studies indicated that Ca2+ binding stabilizes the RCK domains in this octameric state.     

Gas chromatography-mass spectrometric analysis of hexanal and heptanal in human blood by headspace single-drop microextraction with droplet derivatization

In this work, we developed a new approach to the analysis of the lung cancer biomarkers, hexanal and heptanal in human blood that was based on headspace single-drop microextraction (HS-SDME) with droplet derivatization, followed by gas chromatography-mass spectrometry (GC-MS). Aldehydes in blood were headspace extracted, concentrated, and derivatized by a suspended microdrop solvent containing the derivatization agent O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine hydrochloride. The aldehyde oximes formed in the microdrop solvent were analyzed by GC-MS. The optimal HS-SDME with droplet derivatization parameters extraction solvent of decane, sample temperature of 40 degrees C, extraction time of 6 min, stirring rate of 1100 rpm, and solvent volume of 2.0 microL were obtained and used for analysis of hexanal and heptanal in blood. The method reproducibility, linearity, recovery, and detection limit were studied and the obtained results demonstrated the method feasibility. Finally, the proposed method was applied to the quantification of hexanal and heptanal in cancer blood and normal blood. Due to sample extraction, concentration, and derivatization being performed in a single step, the method provided a simple, rapid, low-cost, and efficient approach to analysis of aldehydes in blood samples.     

The GUS reporter-aided analysis of the promoter activities of Arabidopsis ACC synthase genes AtACS4, AtACS5, and AtACS7 induced by hormones and stresses

Ethylene biosynthesis in higher plants is regulated developmentallyand environmentally. To investigate the regulation of ACC synthasegene expression, the promoters of Arabidopsis ACS genes, AtACS4,AtACS5, and AtACS7, were fused to a GUS reporter gene, and therecombinant transgenes were introduced into Arabidopsis to producethree groups of AtACS::GUS transgenic plants. Histochemic andfluorometric study of these transgenic plants revealed thatpromoters of AtACS4, AtACS, and AtACS7 are all active in dark-germinatedseedlings. AtACS5 has the highest promoter activity in leavesof 2-week-old light-grown seedlings among the three AtACS genesstudied. In the mature leaves, AtACS4 and AtACS7 genes are expressedin both veins and areoles, whereas AtACS5 is expressed at ahigher level in the areoles and epidermal cells surroundingtrichomes. The promoter activities of all these AtACS genesare found in the reproductive organs. AtACS5 and AtACS7 arehighly expressed in petals, sepals, carpels, stamens, caulineleaves, inflorescence stems, and siliques, while AtACS4 expressionis undetectable in the petals of open flowers. All three AtACSgenes are expressed in root tissue. In the 2-week-old light-grownArabidopsis, the AtACS4 promoter is responsive to the planthormones IAA, ethylene, and ABA, and to darkness and wounding;the AtACS5 promoter to IAA, ABA, salt, high temperature, andwounding; and the AtACS7 promoter to GA₃, ethylene, and ABA,and to darkness and salt. Low-temperature treatment abolishesthe darkness-induced AtACS7 gene expression, but not that ofAtACS4. Each AtACS gene has a unique expression profile duringgrowth and development. It appears that at any developmentalstage or any growth period of Arabidopsis, there is always amember of AtACS multigene family that is actively expressed. Key words: ACC synthase, Arabidopsis, ethylene, gene expression, GUS histochemical staining, reporter, stress treatments     

Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc-binding module

Kti11p is a small, highly conserved CSL zinc finger-containing protein found in many eukaryotes. It was first identified as one of the factors required for maintaining the sensitivity of Saccharomyces cerevisiae to Kluyveromyces lactis zymocin. Then, it was found to be identical to Dph3, a protein required for diphthamide biosynthesis on eEF-2, the target of diphtheria toxin and Pseudomonas exotoxin A, in both yeast and higher eukaryotes. Furthermore, Kti11p/Dph3 was found to physically interact with core-Elongator, ribosomal proteins, eEF-2, two other proteins required for diphthamide modification on eEF-2, and DelGEF. Here, we determined the solution structure of Kti11p using NMR, providing the first structure of the CSL-class zinc-binding protein family. We present the first experimental evidence that Kti11p can bind a single Zn(2+) ion by its four conserved cysteine residues. The major structure of Kti11p comprises a beta sandwich as well as an alpha helix. Moreover, a structure-based similarity search suggests that it represents a novel structure and may define a new family of the zinc ribbon fold group. Therefore, our work provides a molecular basis for further understanding the multiple functions of Kti11p/Dph3 in different biological processes.