Stimulation of the Biosynthesis of the Antibiotics Lambertellols by the Mycoparasitic Fungus Lambertella corni-maris under the Acidic Conditions Produced by Its Host Fungus in Vitro

The filamentous fungus, Lambertella corni-maris (L. corni-maris), a mycoparasite on Monilinia fructigena, produces the antibiotics, lambertellols A (1), B (2), and lambertellin (3), in a substantial amounts under acidic conditions, whereas these antibiotics were hardly detected when the fungus was cultured on a potato-sucrose (PS) medium without added acids. Our investigations also revealed that the host, M. fructigena, changed its surroundings into acidic conditions, suggesting that the acidic conditions acted as kairomones that stimulated the production of 1–3.     

Sensitive and resistant of the homologous disulfide-bridged proteins α-lactalbumin and lysozyme to attack of hydrogen-atoms,dithiothreitol and trifluoroacetic acid,examined by matrix-assisted laser desorption/ionization mass spectrometry

BackgroundEvolutionarily homologous proteins bovine α-lactoalbumin (αLA) and hen egg-white lysozyme (HEL) are very similar in primary, secondary and tertiary structures involving the location of disulfide-bridges (S–S), and are resistant to the action of hydrolytic enzymes and reagents. It is of interest to examine and compare the difference in backbone cleavage characteristics, by using reductive and hydrolytic reagents.MethodsIn-source decay (ISD) combined with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), reductive treatment of αLA and HEL with dithiothreitol (DTT) and acid hydrolysis with trifluoroacetic acid (TFA) were employed to examine the difference in the backbone cleavage characteristics of αLA and HEL.ResultsThe treatment of αLA and HEL with DTT/AcOHNH₃ resulted in similar cleavage behaviors of the backbone N-Cα and S–S bonds, i.e., the enhancements of the intensity and m/z range of sequence-reflected fragment ions were very similar. However, the treatment of αLA with DTT/TFA resulted in unexpected residue-specific degradation at the peptide bond of the Asp-Xxx, Xxx-Ser/Thr, Gln-Xxx, Xxx-Gly and Gly-Xxx residues, while HEL did not occur such degradation.ConclusionsThe results obtained above indicate that acidic αLA is very sensitive to acidic additive such as TFA, while basic HEL is resistance to acidic additives.General significanceThe study demonstrates the sensitive and resistant of evolutionary homologous proteins αLA and HEL to the acid hydrolysis and these characters come from acidic and basic nature of the proteins.     

Direct visualization of avian influenza H5N1 hemagglutinin precursor and its conformational change by high-speed atomic force microscopy

BackgroundHemagglutinin (HA) of influenza A is one of the key virulence factors that mediates the release of viral components in host cells. HA is initially synthesized as a trimeric precursor (HA0) and then it is cleaved by proteases to become a functional HA. Low pH induces irreversible conformational changes in both HA0 and HA but only HA is fusion compatible. Here, we used high-speed atomic force microscopy (HS-AFM) to record conformational changes in HA0 trimers (H5N1) from neutral to acidic conditions at a millisecond scale.MethodsPurified HA0 protein was diluted with either neutral Tris-HCl (pH 7.4) or acetic acid-titrated Tris-HCl (pH 5.0) and then loaded onto bare mica. Neutral or acidic Tris-HCl was used as the scanning buffer. HS-AFM movies were recorded and processed using Image J software.ResultsThe conformation of HA0_neutral visualized using HS-AFM was comparable to the HA trimer structures depicted in the PDB data and the AFM simulator. HA0 underwent rapid conformational changes under low pH condition. The circularity and area of HA0_acid were significantly higher than in HA0_neutral. In contrast, the height of HA0_acid was significantly lower than in HA0_neutral.ConclusionsWe have captured real-time images of the native HA0 trimer structure under physiological conditions using HS-AFM. By analyzing the images, we confirm that HA0 trimer is sensitive to acidic conditions.General significanceThe dynamic nature of the HA structure, particularly in the host endosome, is essential for H5N1 infectivity. Understanding this acidic behavior is imperative for designing therapeutic strategies against H5N1. This article reports a sophisticated new tool for studying the spatiotemporal dynamics of the HA precursor protein.     

Plant richness and composition in hardwood forest understories vary along an acidic deposition and soil-chemical gradient in the northeastern United States

Aims

A century of atmospheric deposition of sulfur and nitrogen has acidified soils and undermined the health and recruitment of foundational tree species in the northeastern US. However, effects of acidic deposition on the forest understory plant communities of this region are poorly documented. We investigated how forest understory plant species composition and richness varied across gradients of acidic deposition and soil acidity in the Adirondack Mountains of New York State.

Methods

We surveyed understory vegetation and soils in hardwood forests on 20 small watersheds and built models of community composition and richness as functions of soil chemistry, nitrogen and sulfur deposition, and other environmental variables.

Results

Community composition varied significantly with gradients of acidic deposition, soil acidity, and base cation availability (63% variance explained). Several species increased with soil acidity while others decreased. Understory plant richness decreased significantly with increasing soil acidity (r?=?0.60). The best multivariate regression model to predict richness (p?<?0.001, adjusted-R²?=?0.60) reflected positive effects of pH and carbon-to-nitrogen ratio (C:N).

Conclusions

The relationship we found between understory plant communities and a soil-chemical gradient, suggests that soil acidification can reduce diversity and alter the composition of these communities in northern hardwood forests exposed to acidic deposition.

     

酸性旱地红壤无机氮同化菌株筛选及其全基因组分析

微生物执行的无机氮同化作用可固定施入土壤后未被作物直接吸收的化学氮肥,有效减少化学氮肥损失、降低环境氮素污染风险。土壤无机氮同化作用不是由大量冗余微生物共同执行的,而是由一小部分功能微生物优先执行。【目的】对酸性旱地红壤中的优势无机氮同化细菌进行富集、菌株分离鉴定及全基因组测序,并明确菌株在土壤中的氮同化能力,为酸性土壤化学氮肥应用及其转化过程研究提供菌株资源和理论依据。【方法】在酸性旱地红壤中添加KNO3或(NH4)2SO4作为无机氮源,以葡萄糖作为碳源,在好氧条件下进行富集预培养,采用稀释分离法筛选出优势无机氮同化细菌菌株;将菌株回接至土壤中从而验证其无机氮同化能力,并通过全基因组测序分析菌株的氮素代谢途径及相关功能基因。【结果】酸性旱地红壤经富集预培养一周后,优势无机氮同化微生物的16SrRNA基因相对丰度从0.20%–0.94%增长至20.2%–30.2%;分离筛选后得到的3株优势无机氮同化细菌菌株,鉴定为伯克霍尔德氏菌(Burkholderia sp.) M6-3、索状芽孢杆菌(Bacillus funiculus) M2-4和节杆菌(Arthrobacter sp.) M7...     

乙酰化修饰降低Ku蛋白的DNA结合活性

【目的】研究乙酰化修饰对Ku蛋白活性的影响。【方法】利用耻垢分枝杆菌为表达菌株,转入Ku蛋白表达质粒,纯化具有乙酰化修饰的Ku蛋白和无乙酰化的Ku蛋白突变体,比较两类蛋白的生化活性;分析氧化压力和酸性环境下耻垢分枝杆菌细胞内Ku蛋白乙酰化水平的变化。【结果】Ku蛋白过量表达的耻垢分枝杆菌比转入空质粒的对照菌株生长缓慢;乙酰化Ku蛋白比未发生乙酰化Ku蛋白修复断裂DNA的活性降低、DNA结合活性降低;氧化压力和酸性压力环境下,耻垢分枝杆菌细胞内Ku蛋白数量降低,乙酰化Ku蛋白数量变化不大。【结论】乙酰化修饰能够调节Ku蛋白的DNA结合活性,从而调节非同源末端连接修复系统的活性;Ku蛋白乙酰化程度升高是耻垢分枝杆菌对不良生长环境的反应。     

Doped Natural Phosphate: A New and Environmentally Friendly Catalyst in Nucleoside Synthesis

Abstract

Doped natural phosphate is used as acidic or basic catalyst in nucleoside and acyclonucleoside synthesis. Some examples are given.     

An anti-HBV anthraquinone from aciduric fungus Penicillium sp. OUCMDZ-4736 under low pH stress

To obtain new bioactive natural products, the effect of acidic stress on the metabolites of an aciduric fungus was investigated. This fungus, Penicillium sp. OUCMDZ-4736, which was isolated from the sediment around roots of mangrove (Acanthus ilicifolius), produced different compounds and higher yields under pH 2.5 than under neutral conditions. Using spectroscopic analyses and calculations, three new anthraquinone derivatives (1–3) were isolated and identified from the acidic fermentation broth (pH 2.5) of OUCMDZ-4736. Compound 1 showed much stronger anti-hepatitis B virus activity than that of the positive control, lamivudine, strongly inhibiting HBsAg and HBeAg secretion from HepG2.2.15 cells. These results show that extremophiles are a valuable resource of bioactive compounds, and that pH regulation is an effective strategy to induce metabolite production in aciduric fungi.

     

Syntheses of 2′-O-Methylisocytidine Phosphoramidite and Methylphosphonamidite Synthons

Abstract

The 2′-O-methylisocytidine phosphoramidite synthon 7 and methylphosphonamidite synthon 8 are synthesized from 2′-O-methyluridine. The N² -(N′, N′-dimethylformamidine) protected 2′-O-methylisocytidine is stable to basic deamination and acidic depyrimidination. Synthon 7 and synthon 8 have been incorporated into oligomers via the automated solid state procedure.

     

Preparation,Hydrolysis and Intramolecular Transesterification of 3′-Deoxy-3′-thioinosine 3′-S-Dimethylphosphorothiolate

Abstract

The hydrolytic reactions of the dimethyl ester of 3′-deoxy-3′-thioinosine 3′-S-phosphorothiolate have been followed over a wide aciditty range by HPLC. At pH > 3, only hydroxide ion catalyzed isomerization to the 2′-dimethylphosphate takes place, whereas under more acidic conditions hydrolysis to the 2′-monomethylphosphate and 3′-S-monomethylphosphorothiolate competes. The latter is the only product accumulating in very acidic solutions (1 M hydrochloric acid). Mechanisms of the reactions are discussed.     

PPEF: A bisbenzimdazole potent antimicrobial agent interacts at acidic triad of catalytic domain of E. coli topoisomerase IA

BackgroundTopoisomerase is a well known target to develop effective antibacterial agents. In pursuance of searching novel antibacterial agents, we have established a novel bisbenzimidazole (PPEF) as potent E. coli topoisomerase IA poison inhibitor.MethodsIn order to gain insights into the mechanism of action of PPEF and understanding protein-ligand interactions, we have produced wild type EcTopo 67 N-terminal domain (catalytic domain) and its six mutant proteins at acidic triad (D111, D113, E115). The DDE motif is replaced by alanine (A) to create three single mutants: D111A, D113A, E115A and three double mutants: D111A-D113A, D113A-E115A and D111A-E115A.ResultsCalorimetric study of PPEF with single mutants showed 10 fold lower affinity than that of wild type EcTopo 67 (7.32 × 10⁶ M⁻¹for wild type, 0.89 × 10⁶ M⁻¹for D111A) and 100 fold lower binding with double mutant D113A-E115A (0.02 × 10⁶ M⁻¹) was observed. The mutated proteins showed different CD signature as compared to wild type protein. CD and fluorescence titrations were done to study the interaction between EcTopo 67 and ligands. Molecular docking study validated that PPEF has decreased binding affinity towards mutated enzymes as compared to wild type.ConclusionThe overall study reveals that PPEF binds to D113 and E115 of acidic triad of EcTopo 67. Point mutations decrease binding affinity of PPEF towards DDE motif of topoisomerase.General significanceThis study concludes PPEF as poison inhibitor of E. coli Topoisomerase IA, which binds to acidic triad of topoisomerase IA, responsible for its function. PPEF can be considered as therapeutic agent against bacteria.     

Preparation of polymer-bound trityl-hydrazines and their application in the solid phase synthesis of partially protected peptide hydrazides

Summary Polymer-bound N-tritylhydrazines 4 were easily prepared by reacting polymeric tritylchlorides 3 with hydrazine. Subsequently, compounds 4 have been successfully applied to the solid phase synthesis of partially protected peptide hydrazides using 1-hydroxybenzotriazolyl esters of Fmoc- or Trt-amino acids. The synthesized peptide hydrazides can be quantitatively split off from the resins by mild acidic treatment, while the benzyl- and tert-butyl protecting groups remain unaffected.     

9-(2-Deoxy-ß-D-xylofuranosyl)adenine and 1-(2-Deoxy-ß-D-xylofuranosyl)thymine: Phosphorylation and Stability

Abstract

Phosphorylation of 1-(2-deoxy-β-D-xylofuranosyl)thymine (1) or 9-(2-deoxy-β-D-xylofuranosyl)adenine (3) with phosphoryl chloride gives the cyclic 3′,5′-phosphates (2 and 4a) but not the 5′-monophosphates 8a or 8b. The latter are obtained by phosphorylation of the 3′-0-benzoylated 2′-deoxy-β-D-xylonucleosides (7a, b) and subsequent base-catalyzed removal of the benzoyl groups. Compound 3, as the parent dA, depurinates in acidic medium, a reaction which is facilitated in the case of the N⁶-benzoyl derivative 9b and reduced after the introduction of an amidine protecting group. N-Glycosylic bond hydrolysis of 2′-deoxy-β-D-xylofuranosyl nucleosides is enhanced by a factor of two compared to 2′-deoxy-β-D-ribofuranosyl nucleosides.     

Reevaluation of the Subunit Molecular Weights of Soybean 11S Globulin

The acidic and basic subunits are the main constituents of soybean 11S globulin. Each of these two subunits consists of three major polypeptides of similar size. The molecular weights of the acidic and basic subunits have been previously estimated to be 37,000 and 22,000, respectively, by SDS-polyacrylamide gel electrophoresis (Catsimpoolas et al, J. Set Food. Agric., 22, 448 (1971)). Reevaluation of the molecular weights by 6 m guanidine gel chromatography gave the values of 28,000 and 18,000, respectively. These are supported by results of equilibrium sedimentation in the same solvent. The previously reported values seem to have been overestimated, especially for the acidic subunits. The overestimations seem to be related to the high percentage of acidic amino acids, which causes the conformation of the SDS-protein polypeptide complexes of these subunits to deviate from those of proteins usually employed as standards for molecular weight estimations.     

安徽某铁矿不同矿山废水库中微生物群落结构特征

【目的】研究安徽某铁矿不同矿山废水库中微生物群落结构特征及其影响因素。【方法】对比分析了该铁矿3个大型废水库的地球化学特征,并用高通量测序技术研究了水体中微生物群落组成,进而用统计学方法解析了环境因子对微生物群落结构的影响。【结果】3个废水库中有2个为酸性,1个为中性,理化性质有明显的差异。近年形成的塌方采场废水库(TF) pH仅为2.55±0.01,Fe浓度高达154.95±0.78mg/L,SO_4~(2–)浓度为3374.86±3.81mg/L;形成于20世纪70年代的排土场废水库(PT)酸性略弱(pH 2.9±0.02),Fe浓度(34.57±4.00 mg/L)与TF相比明显降低,SO_4~(2–)浓度则高达10398.98±626.70 mg/L;东沙采场废水库(DS)则为中性(pH7.55),但SO_4~(2–)仍高达4162.99mg/L,主要的金属离子为Mg(594.90 mg/L)、Ca (650.10 mg/L)。3个废水库的原核生物多样性随pH的升高而升高。两个酸性废水库的原核生物组成较为接近,但TF的化能自养菌含量较高(69.54%±2.89%),PT的化能异养菌含量较高(64.45%±13.81%)。自养铁氧化菌Ferrovum在TF中的比例高达(64.17±1.84)%,在PT中则下降为(35.39±13.74)%。但PT中含有丰富的化能异养嗜酸菌如Acidicapsa(15.75%±3.99%)、Acidiphilium(10.65%±2.05%)、Acidisphaera (6.34%±1.02%)等。DS中虽然也含有较高的金属离子和SO_4~(2–),但其中的原核生物组成与TF和PT截然不同,主要为Limnohabitans (18.47%)、Rhodobacter (8.42%)等。3个废水库的真核生物群落主要由藻类组成,酸水库TF和PT中主要为棕鞭藻属(Ochromonas)和胶球藻属(Coccomyxa),棕鞭藻属在TF中(53.65%±2.02%)占优势,胶球藻属在PT中(68.84±10.4%)占优势,中性废水库DS中则主要是小环藻属(Cyclotella)(49.85%)。经统计学分析,pH是影响矿山废水微生物多样性和群落组成的主要环境因素。     

Environmental pH modulates biofilm formation and matrix composition in Candida albicans and Candida glabrata

Abstract

Candida species are fungal opportunistic pathogens capable of colonizing and infecting various human anatomical sites, where they have to adapt to distinct niche-specific pH conditions. The aim of this study was to analyse the features of Candida albicans and Candida glabrata biofilms developed under neutral and vaginal acidic (pH 4) conditions. C. albicans produced thicker and more filamentous biofilms under neutral than under acidic conditions. On the other hand, the formation of biofilms by C. glabrata was potentiated by the acidic conditions suggesting the high adaptability of this species to the vaginal environment. In general, both species developed biofilms containing higher amounts of matrix components (protein and carbohydrate) under neutral than acidic conditions, although the opposite result was found for one C. glabrata strain. Overall, this study contributes to a better understanding of the modulation of C. albicans and C. glabrata virulence by specific pH conditions.     

In vitro digestion method to evaluate solubility of dietary zinc,selenium and manganese in salmonid diets

BackgroundThe determination of dietary mineral solubility is one of the main steps in the evaluation of their availability for a given species.MethodsThis study proposed an in vitro digestion method (acidic and alkaline hydrolysis). The method was applied to evaluate the solubility of inorganic and organic forms of zinc (Zn), selenium (Se) and manganese (Mn) in salmonid diets. An inorganic mineral (IM) diet was supplemented with zinc sulphate, sodium selenite and manganous sulphate and an organic mineral (OM) diet was supplemented with zinc chelate of glycine, l-selenomethionine and manganese chelate of glycine.ResultsThe solubility of Zn was similar in both diets tested. The amount of soluble Zn was low in the acidic hydrolysis (3–8%) and lower in the alkaline hydrolysis (0.4–2%). The solubility of Se was higher in the OM diet (7–34%) compared with the IM diet (3–12%). Regarding Mn, after the acidic hydrolysis the solubility was higher in the IM diet (6–25%) than the OM diet (4–17%). The in vitro solubility were compared with in vivo availability of Zn, Se and Mn. Data obtained for solubility (%) of Zn, Se and Mn was lower when compared with apparent availability (%) of Zn, Se and Mn.ConclusionData obtained demonstrated that solubility of Zn, Se and Mn was influenced by the mineral chemical form supplemented to the diet and by the gastrointestinal environment. The solubility of Zn, Se and Mn was not comparable with the apparent availability of Zn, Se and Mn. Nevertheless, the effect of the chemical form of the minerals was similar for the solubility of Zn, Se and Mn and the apparent availability of Zn, Se and Mn. Considering the overall results of this study, the in vitro method could replace some of the in vivo studies for a qualitative evaluation but not for a quantitative evaluation.     

Reversible aggregation of mouse prion protein derivatives with PrPSC-like structural properties

Three carbamylated derivatives of reduced mouse prion protein (mPrP) were isolated during the aborted oxidative folding in the presence of urea. These three prion protein derivatives (mPrP-a, mPrP-b, and mPrP-c) exist as monomer in the acidic solution (pH < 2.0) and exhibit prevalent random coil structure. However, they undergo rapid aggregation and transformation to a predominant -sheet structure upon exposure to ionic buffer with pH greater than 3.0. The stability of aggregates of mPrP conformers is in part dependent upon the time that they were allowed to develop. The nascent aggregates comprise a significant fraction of loosely packed mPrP monomers that can be dissociated by treatment with strong acidic solution. Matured aggregates acquired through prolonged sample incubation contain more tightly packed mPrP monomers that cannot be dissociated by strong acid but can be disaggregated by denaturant. The properties of reversible aggregation of mPrP-a, mPrP-b, and mPrP-c bear a striking resemblance to that observed with aggregates of hamster PrP^SC.     

4-Cyano-2-butenyl Group: A New Type of Protecting Group in Oligonucleotide Synthesis via Phosphoramidite Approach

Abstract

4-Cyano-2-butenyl (CB) is a new type of protecting group for the intemucleotidic bonds in the synthesis of oligodeoxyribonucleotides by the phosphoramidite approach. This group is stable to acidic conditions and can be removed under mild conditions by a δ-elimination pathway using aqueous ammonium hydroxide.     

Enhancing and Sustaining AMG 009 Dissolution from a Bilayer Oral Solid Dosage Form via Microenvironmental pH Modulation and Supersaturation

Enhancing and sustaining AMG 009 dissolution from a matrix tablet via microenvironmental pH modulation and supersaturation, where poorly soluble acidic AMG 009 molecule was intimately mixed and compressed together with a basic pH modifier (e.g., sodium carbonate) and nucleation inhibitor hydroxypropyl methylcellulose K100 LV (HPMC K100 LV), was demonstrated previously. However, not all acidic or basic drugs are compatible with basic or acidic pH modifiers either chemically or physically. The objective of this study is to investigate whether similar dissolution enhancement of AMG 009 can be achieved from a bilayer dosage form, where AMG 009 and sodium carbonate are placed in a separate layer with or without the addition of HPMC K100 LV in each layer. Study results indicate that HPMC K100 LV-containing bilayer dosage forms gained similar dissolution enhancement as matrix dosage forms did. Bilayer dosage forms without HPMC K100 LV benefitted the least from dissolution enhancement.