Characterization of a Highly Conserved Binding Site of Mlh1 Required for Exonuclease I-Dependent Mismatch Repair

Mlh1 is an essential factor of mismatch repair (MMR) and meiotic recombination. It interacts through its C-terminal region with MutL homologs and proteins involved in DNA repair and replication. In this study, we identified the site of yeast Mlh1 critical for the interaction with Exo1, Ntg2, and Sgs1 proteins, designated as site S2 by reference to the Mlh1/Pms1 heterodimerization site S1. We show that site S2 is also involved in the interaction between human MLH1 and EXO1 or BLM. Binding at this site involves a common motif on Mlh1 partners that we called the MIP-box for the Mlh1 interacting protein box. Direct and specific interactions between yeast Mlh1 and peptides derived from Exo1, Ntg2, and Sgs1 and between human MLH1 and peptide derived from EXO1 and BLM were measured with K_d values ranging from 8.1 to 17.4 μM. In Saccharomyces cerevisiae, a mutant of Mlh1 targeted at site S2 (Mlh1-E682A) behaves as a hypomorphic form of Exo1. The site S2 in Mlh1 mediates Exo1 recruitment in order to optimize MMR-dependent mutation avoidance. Given the conservation of Mlh1 and Exo1 interaction, it may readily impact Mlh1-dependent functions such as cancer prevention in higher eukaryotes.     

Light activation of NADH and NADPH]

Illumination of NADH and NADPH by UV-light in the absence of oxygen resulted in the reduction of ferredoxin or methyl-viologen to cation-radical and under prolonged illumination to dihydrodipyridyl. The reaction may by accompanied by triplet and singlet exitation of NADH. It was shown that hematoporphyrin in aqueous solution photosensitized the reaction of NADH oxidation by ferredoxin and methylviologen to the visible region of the spectrum. Under light excitation the redox potentials of NADH and NADPH were increased up to the level exceeding the potential of hydrogen electrode. Illumination of NADH and NADPH by UV-light in the presence of bacterial hydrogenase resulted in hydrogen evolution. The reaction of hydrogen evolution could be sensitised towards the visible region of the spectrum by chlorophyll or chloroplasts.     

ESR signals of NADH and NADPH under illumination

ESR method was applied to investigate the formation of NADH and NADPH free radicals. It was shown that under the action of light (340 nm) in water and other solutions of these compounds a reaction occurred resulting in the formation of free radicals having the typical ESR spectrum. The analysis of the temperature dependence showed the light-induced ESR signals to be registered at −30°C to −120°C, the most intensive ones being observed at −50°C. It was concluded that the observed ESR signals belonged to the products of one-electron oxidation of the coenzymes-free radicals NAD^. and NADP^..     

NADH and NADPH Dependent Malate Dehydrogenases of Phaseolus vulgaris

French bean (Phaseolus vulgaris L. cv. Contender) leaf extracts catalyse the reduction of oxaloacetate to malate in the presence of NADH and NADPH. Under the experimental conditions used, the optimum pH values are 8 and 6 respectively. After chromatography on diethylaminoethyl cellulose, two principal forms of NADH-MDH (L-malate: NAD⁺ oxidoreductase, E.C. 1.1.1.37) upon which NADPH activities are superposed, can be characterized. This result is confirmed by electrophoresis on polyacrylamide gel. On the other hand, after filtration on Ultrogel 34, NADH-MDH is eluted as a single peak; once again, NADPH activity is associated with it. When PtCl^2?₄, a powerful inhibitor of MDH, is added to the reaction medium, the degree of inhibition is the same irrespective of the cofactor employed. When root extracts are submitted to chromatography on diethylaminoethyl cellulose, activity profiles are identical to those obtained with leaves. These results suggest that the NAD dependent enzymes can also utilize NADP to reduce oxaloacetate. After addition of dithiothreitol, another NADPH-MDH activity manifests itself in the leaf extracts; it differs from the foregoing ones in its optimum pH, its chromatographic properties and its response to PtCl^2?₄ action. Root extracts do not exhibit this activity thus showing a specific localization of this enzyme in the green part of the plant.     

Utilization of substrate-induced quenching for screening targets promoting NADH and NADPH consumption

Oxidation of reduced nicotinamide adenine dinucleotides is a common event for many biochemical reactions. However, its exploitation for ultrahigh-throughput screening purposes is not an easy task and is affected by various drawbacks. It is known that such nucleotides induce quenching on the fluorescence of several dyes and that this quenching disappears with oxidation of the nucleotide. We have made use of this property to develop an assay for high-throughput screening with NADH and NADPH-dependent reductases. Full screening campaigns have been run with excellent assay quality parameters, and interesting hits have been identified. The method is amenable to miniaturization and allows easy identification of false positives without needing extra secondary assays. Although it is based on monitoring substrate consumption, it is demonstrated that the effect of fractional conversion on assay sensitivity is negligible.     

Identification of a Highly Conserved Surface on Tat Variants

Extracellular Tat is suspected to protect HIV-1-infected cells from cellular immunity. Seropositive patients are unable to produce neutralizing antibodies against Tat, and Tat is still secreted under antiviral treatment. In mice, the Tat OYI vaccine candidate generates neutralizing antibodies such as the mAb 7G12. A peptide called MIMOOX was designed from fragments of Tat OYI identified as the possible binding site for mAb 7G12. MIMOOX was chemically synthesized, and its structure was stabilized with a disulfide bridge. Circular dichroism spectra showed that MIMOOX had mainly β turns but no α helix as Tat OYI. MIMOOX was recognized by mAb 7G12 in ELISA only in reduced conditions. Moreover, a competitive recognition assay with mAb 7G12 between MIMOOX and Tat variants showed that MIMOOX mimics a highly conserved surface in Tat variants. Rat immunizations with MIMOOX induce antibodies recognizing Tat variants from the main HIV-1 subtypes and confirm the Tat OYI vaccine approach.     

Photokinetic assay of NADH and NADPH in microdissected tissue samples

A high sensitivity is reached in photokinetic assay of reduced pyridine nucleotides with extracts of Achromobacter fischerii. When occurring together, NADH and NADPH are difficult to measure individually, since both initiate light emission. This problem has been solved by selective enzymic oxidation of either nucleotide before the measurement of the other. Assay of the reduced nucleotides in extracts of microdissected samples from pancreatic islets, exocrine pancreas, and liver demonstrates the applicability of the methods.     

NADH and NADPH dehydrogenases from the blue-green alga,Aphanocapsa

Two different NAD(P)H dehydrogenases could be demonstrated in the blue-green alga, Aphanocapsa. Both function as quinone reductases using benzoquinone as electron acceptor. One, which was found in the soluble fraction, was NADH specific and showed high sensitivity to rotenone, thenoyltrifluoroacetone and o-phenanthroline. The second dehydrogenase was membrane-bound and used NADH as well as NADPH as substrates. Inhibition by rotenone and o-phenanthroline was less pronounced with the bound enzyme than with the soluble enzyme. Based on studies with NADH or NADPH, the membrane-bound enzyme apparently was associated with a low-temperature EPR signal at g=1.92 in the reduced state, indicative of an iron-sulfur center. The membrane-bound dehydrogenase was solubilized with Triton X-100 and partially purified. This preparation was used for studies of enzyme kinetics and acceptor specificity.Abbreviations DBMIB 2,5-dibromo methyl isopropylbenzoquinone - TTFA thenoyltrifluoroacetone - E_m midpoint redox potential     

Interaction of zinc ions with electron carrying coenzymes NADPH and NADH

Evidence is presented that the substrate for the drug oxidizing system, NADPH, binds to zinc ions. Zinc ions bind selectively to NADPH but not to NADH. By using equilibrium gel filtration and acid titrations of Zn²⁺ and NADPH, the molar ratio of metal to nucleotide was determined at 2 : 1, as well as the formation constant of 10^6.75. Results from ³¹P-nuclear magnetic resonance (NMR), ultraviolet and fluorescence spectra of the complex indicated the possible binding sites of zinc to NADPH.In previous studies we have shown that zinc ions inhibit the metabolism of drugs by mixed function oxidases in liver microsomes. The formation of the Zn²⁺-NADPH complex suggests the mechanism by which zinc ions may inhibit the drug oxidizing system.     

一种转基因植物高特异定性检测方法

近年来,植物基因工程技术的迅速发展使得转基因植物及其产品与人们生活越来越密切.与此同时,转基因植物检测技术不断丰富和发展,主要是在整合、转录、翻译等不同水平上检测转基因产物的存在.但各种方法都存在不同的缺点,如缺乏特异性、假阳性较高,操作繁琐、成本高等.利用TAIL-PCR(thermal asym-metric interlaced PCR)和融合克隆结合建立一种简单、快速、特异性高的转基因植物检测方法,以两个转基因植株(C3-3株系和TB-5株系)为例,通过TAIL-PCR获得其侧翼序列后设计特异引物,并用于特定转基因植株的筛选.     

一组高度保守的水稻trs-like基因的鉴定与分析

基于对水稻基因组序列的注解和同源搜索的结果,用RT-PCR结合测序的方法证明了水稻中至少有10个具有转录活性的trs-like基因。这10个基因的编码产物与酵母TRAPP蛋白复合体已知10个亚基中的6个分别同源。其中4对基因是双拷贝的,另2个则是单拷贝的(基于已知的水稻基因组序列)。所有这10个基因均在不同时期的水稻组织中广泛表达,并与其他真核生物的trs-like基因在基因结构及编码蛋白质序列水平上高度保守。     

Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

Background

Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown.

Results

To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains.

Conclusion

HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.     

Negative modulation of Escherichia coli NAD kinase by NADPH and NADH.

NAD kinase was purified 93-fold from Escherichia coli. The enzyme was found to have a pH optimum of 7.2 and an apparent Km for NAD+, ATP, and Mg2+ of 1.9, 2.1, and 4.1 mM, respectively. Several compounds including quinolinic acid, nicotinic acid, nicotinamide, nicotinamide mononucleotide, AMP, ADP, and NADP+ did not affect NAD kinase activity. The enzyme was not affected by changes in the adenylate energy charge. In contrast, both NADH and NADPH were potent negative modulators of the enzyme, since their presence at micromolar concentrations resulted in a pronounced sigmoidal NAD+ saturation curve. In addition, the presence of a range of concentrations of the reduced nucleotides resulted in an increase of the Hill slope (nH) to 1.7 to 2.0 with NADH and to 1.8 to 2.1 with NADPH, suggesting that NAD kinase is an allosteric enzyme. These results indicate that NAD kinase activity is regulated by the availability of ATP, NAD+, and Mg2+ and, more significantly, by changes in the NADP+/NADPH and NAD+/NADH ratios. Thus, NAD kinase probably plays a role in the regulation of NADP turnover and pool size in E. coli.     

The effect of o-diphenols upon the microsomal NADPH and NADH oxidase activities

Catechol and catecholamines have been assayed upon the microsomal NADPH and NADH oxidase activities. Epinephrine shows a catalytic effect on the NADPH oxidation characterized by a small lag. The two to threefold increase in rate can be suppressed by Superoxide dismutase if the enzyme is added before the reaction begins. The catalytic effect is ascribed to a quinone formed by two electron oxidation of epinephrine by the Superoxide ion. The quinone, which is not catalytically active in the NADH chain, appears to mediate electrons between the NADPH-cytochrome c reductase and oxygen. The four electron oxidation product adrenochrome is also active upon the NADPH chain but inactive upon the NADH chain.Epinephrine did not change the menadione-stimulated NADPH oxidase activity. Presumably, during this and the NADH oxidase activities, two electrons are simultaneously transferred to the oxygen molecule.Catechol and catecholamines doubled the rate of autoxidation of NADH in the presence of catalytic amounts of NADH-cytochrome b₅ reductase and cytochrome b₅, a result which suggests Superoxide ion formation in the autoxidation of the cytochrome.Epinephrine does not act upon the desaturation of endogenous substrate or upon endogenous lipid peroxidation.