Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template

Transfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3' end of tRNAs by means of the addition of the essential nucleotides CCA. However, it is unclear how tRNA nucleotidyltransferases polymerize CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template. Here we describe the crystal structure of the Archaeoglobus fulgidus tRNA nucleotidyltransferase in complex with tRNA. We also present ternary complexes of this enzyme with both RNA duplex mimics of the tRNA acceptor stem that terminate with the nucleotides C74 or C75, as well as the appropriate incoming nucleoside 5'-triphosphates. A single nucleotide-binding pocket exists whose specificity for both CTP and ATP is determined by the protein side chain of Arg 224 and backbone phosphates of the tRNA, which are non-complementary to and thus exclude UTP and GTP. Discrimination between CTP or ATP at a given addition step and at termination arises from changes in the size and shape of the nucleotide binding site that is progressively altered by the elongating 3' end of the tRNA.     

Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase

The enzyme F1-ATPase has been shown to be a rotary motor in which the central gamma-subunit rotates inside the cylinder made of alpha3beta3 subunits. At low ATP concentrations, the motor rotates in discrete 120 degrees steps, consistent with sequential ATP hydrolysis on the three beta-subunits. The mechanism of stepping is unknown. Here we show by high-speed imaging that the 120 degrees step consists of roughly 90 degrees and 30 degrees substeps, each taking only a fraction of a millisecond. ATP binding drives the 90 degrees substep, and the 30 degrees substep is probably driven by release of a hydrolysis product. The two substeps are separated by two reactions of about 1 ms, which together occupy most of the ATP hydrolysis cycle. This scheme probably applies to rotation at full speed ( approximately 130 revolutions per second at saturating ATP) down to occasional stepping at nanomolar ATP concentrations, and supports the binding-change model for ATP synthesis by reverse rotation of F1-ATPase.     

Interferon-dependent induction of mRNA activity for (2'-5')oligo-isoadenylate synthetase

At least three different enzymes involved in the regulation of protein synthesis are induced in a variety of cells by interferon (IFN). Sensitive assays for these enzymes have been developed and used to establish the specificity, dose dependence and time course of their induction by IFN. One of these enzymes, the oligo-isoadenylate synthetase E, whose product (2'-5')pppApApA activates the latent ribonuclease F, is increased over 50-fold after IFN treatment. We describe here the assay for an mRNA from IFN-treated mouse L cells, that produces oligo-isoadenylate synthetase activity when injected into Xenopus oocytes. This mRNA is found in the cells only after exposure to IFN. The mRNA increases in mouse L cells with the same time course as the enzyme activity itself. In particular, there is a 3-h lag period between IFN addition and the onset of enzyme and mRNA accumulation. Using anti-IFN antibodies, we show that during this lag period the continued interaction of IFN with the cells is necessary for the full induction of the oligo-isoadenylate synthetase.     

ATP-induced helicase slippage reveals highly coordinated subunits

Helicases are vital enzymes that carry out strand separation of duplex nucleic acids during replication, repair and recombination. Bacteriophage T7 gene product 4 is a model hexameric helicase that has been observed to use dTTP, but not ATP, to unwind double-stranded (ds)DNA as it translocates from 5' to 3' along single-stranded (ss)DNA. Whether and how different subunits of the helicase coordinate their chemo-mechanical activities and DNA binding during translocation is still under debate. Here we address this question using a single-molecule approach to monitor helicase unwinding. We found that T7 helicase does in fact unwind dsDNA in the presence of ATP and that the unwinding rate is even faster than that with dTTP. However, unwinding traces showed a remarkable sawtooth pattern where processive unwinding was repeatedly interrupted by sudden slippage events, ultimately preventing unwinding over a substantial distance. This behaviour was not observed with dTTP alone and was greatly reduced when ATP solution was supplemented with a small amount of dTTP. These findings presented an opportunity to use nucleotide mixtures to investigate helicase subunit coordination. We found that T7 helicase binds and hydrolyses ATP and dTTP by competitive kinetics such that the unwinding rate is dictated simply by their respective maximum rates V(max), Michaelis constants K(M) and concentrations. In contrast, processivity does not follow a simple competitive behaviour and shows a cooperative dependence on nucleotide concentrations. This does not agree with an uncoordinated mechanism where each subunit functions independently, but supports a model where nearly all subunits coordinate their chemo-mechanical activities and DNA binding. Our data indicate that only one subunit at a time can accept a nucleotide while other subunits are nucleotide-ligated and thus they interact with the DNA to ensure processivity. Such subunit coordination may be general to many ring-shaped helicases and reveals a potential mechanism for regulation of DNA unwinding during replication.     

1-芘胺,N-甲基对茴香胺在电子转移停流注射法中反应机理研究

在电子转移停流注射法中通过电子转移,1 芘胺,N 甲基对茴香胺与较稳定的阳离子自由基反应生成活泼的阳离子自由基并偶合.用密度泛函理论(DFT)B3LYP方法,在6 31G 基组下,计算研究了中间产物的几何构型和热力学性质,通过反应过程的能量变化及电荷布居分析推测出其偶合机理.并用电喷雾质谱法检测其偶合产物,实验结果与推测值吻合.     

ATP mediates fast synaptic transmission in mammalian neurons.

In addition to its diverse functions inside cells, ATP can act at several types of cell-surface receptor. One of these (P2X-purinoceptor) is believed to be a ligand-gated cation channel. The presence of P2X receptors on autonomic, sensory and central neurons suggests that ATP might be released to act as a fast excitatory synaptic transmitter. Here we record excitatory synaptic potentials and currents from cultured coeliac ganglion neurons which are mimicked by ATP, blocked by the P2-purinoceptor antagonist suramin, desensitized by alpha,beta-methylene-ATP and unaffected by antagonists acting at nicotine, 5-hydroxytryptamine, N-methyl-D-aspartate (NMDA), non-NMDA glutamate, gamma-aminobutyric acid (GABA), noradrenaline or adenosine receptors. We conclude that ATP is the neurotransmitter at this neuroneuronal synapse.     

Mutations in the active site of Escherichia coli phosphofructokinase

The enzyme-catalysed transfer of a phosphoryl group from ATP is an important reaction in a wide variety of biological processes. We demonstrate here the essential function of an aspartate group in the catalysis of phosphoryl transfer by Escherichia coli phosphofructokinase, and the minor role of an arginine residue. We have used oligonucleotide-directed mutagenesis to replace two amino-acid residues which X-ray analysis has shown to be close to the transferred phosphoryl group and we have analysed the forward and back reactions of the mutant enzymes by steady-state kinetics. Changing Asp 127 to Ser reduced the turnover number by a factor of 18,000 in the forward direction and 3,100 in the back reaction, and the Michaelis constant for fructose 1,6-bisphosphate in the reverse reaction by a factor of 45. This shows that this aspartate is a key residue in the rate enhancement by the enzyme, probably acting as a base in the reaction mechanism, and that it also destabilizes the product complex. Changing Arg 171 to Ser reduced the turnover numbers by about 3.4, showing that this arginine has only a minor effect on the catalysis.     

鲫鱼营养研究进展及其配合饲料营养标准探讨

综述了近年来鲫鱼营养研究的进展.主要包括(1)饲料中蛋白质及氨基酸、脂类、碳水化合物及维生素C、胆碱等维生素和钙、磷、镁、碘等矿物元素的适宜含量(2)不同饲料蛋白源、脂肪源及磷源的消化吸收及糖耐量研究(3)鱼体必需氨基酸组成及其对氨基酸的行为反应(4)消化酶的研究.本文还初步拟订了鲫鱼的配合饲料营养标准.     

An interferon-induced cellular enzyme is incorporated into virions

The mechanisms by which interferon inhibits viral growth are only partially understood. Several enzymatic activities increase in cells shortly after treatment with interferon. One of these enzymes, oligo-isoadenylate synthetase, synthesizes (2'-5') isoadenylate oligomers which strongly stimulate the activity of a cellular ribonuclease, RNase F (ref. 7). Interferon also significantly increases the activity of a protein kinase which phosphorylates the initiation factor eIF-2 and can inhibit in vitro protein synthesis. Such interferon-induced enzymes, which affect RNA and protein metabolism, might be responsible for many of its effects on viruses. Indeed, inhibition of viral protein and RNA synthesis appears to have a major role in the antiviral state. We have now investigated possible interactions of the two enzymes with viral constituents during the course of infection and found that in two different membrane-coated RNA viruses, vesicular stomatitis virus (VSV) and Moloney murine leukaemia virus (M-MuLV), there is an accumulation of the 2'-5') oligo-isoadenylate synthetase (E) in the virions. Most of the enzyme is bound to the virion ribonucleoprotein core. The incorporation of E into the virions suggests a direct involvement of the enzyme in regulation of virus functions.     

Repetitive shuttling of a motor protein on DNA

Many helicases modulate recombination, an essential process that needs to be tightly controlled. Mutations in some human disease helicases cause increased recombination, genome instability and cancer. To elucidate the potential mode of action of these enzymes, here we developed a single-molecule fluorescence assay that can visualize DNA binding and translocation of Escherichia coli Rep, a superfamily 1 DNA helicase homologous to Saccharomyces cerevisiae Srs2. Individual Rep monomers were observed to move on single-stranded (ss)DNA in the 3' to 5' direction using ATP hydrolysis. Strikingly, on hitting a blockade, such as duplex DNA or streptavidin, the protein abruptly snapped back close to its initial position, followed by further cycles of translocation and snapback. This repetitive shuttling is likely to be caused by a blockade-induced protein conformational change that enhances DNA affinity for the protein's secondary DNA binding site, thereby resulting in a transient DNA loop. Repetitive shuttling was also observed on ssDNA bounded by a stalled replication fork and an Okazaki fragment analogue, and the presence of Rep delayed formation of a filament of recombination protein RecA on ssDNA. Thus, the binding of a single Rep monomer to a stalled replication fork can lead to repetitive shuttling along the single-stranded region, possibly keeping the DNA clear of toxic recombination intermediates.     

Electron transfer reactions of piperidine aminoxyl radicals

This review article summarizes the electron transfer reactions of piperidine aminoxyl radicals. Electrochemical studies revealed the single electron transfer nature of piperidine aminoxyl radicals. In solution, piperidine aminoxyl radicals serve as single electron transfer oxidation reagent to react with various biologically interesting molecules such as glutathione, cysteine, ascorbic acid, and amines. The reaction product distribution, reaction kinetics, intermediates, and the reaction features in biological mimic environments including micelles and cyclodextrins were investigated. Oxoammonium salts, the one-electron transfer oxidation products of piperidine aminoxyl radicals, are agents of organic synthesis to selectively generate ketones or di-ketones from alcohols or ketones bearing α-methylene group under mild conditions. The new reactions of oxoammonium salts with aromatic amines, phenols, heterocycles including phenothiazines, papaverine, and bilirubin are also illustrated.     

Anaerobic microbial metabolism can proceed close to thermodynamic limits.

Many fermentative bacteria obtain energy for growth by reactions in which the change in free energy (DeltaG') is less than that needed to synthesize ATP. These bacteria couple substrate metabolism directly to ATP synthesis, however, by classical phosphoryl transfer reactions. An explanation for the energy economy of these organisms is that biological systems conserve energy in discrete amounts, with a minimum, biochemically convertible energy value of about -20 kJ mol-1 (refs 1, 2, 3). This concept predicts that anaerobic substrate decay ceases before the minimum free energy value is reached, and several studies support this prediction. Here we show that metabolism by syntrophic associations, in which the degradation of a substrate by one species is thermodynamically possible only through removal of the end product by another species, can occur at values close to thermodynamic equilibrium (DeltaG' approximately 0 kJ mol-1). The free energy remaining when substrate metabolism halts is not constant; it depends on the terminal electron-accepting reaction and the amount of energy required for substrate activation. Syntrophic associations metabolize near thermodynamic equilibrium, indicating that bacteria operate extremely efficient catabolic systems.     

Electrochemical, photoelectrochemical, electrocatalytic and catalytic reduction of redox proteins

Redox proteins catalyse the reactions of a wide variety of otherwise intractable substrates, such as dinitrogen, alkanes, arenes, terpenes and steroids. Two major factors impede the utilization of these enzymes--the inefficient electron transfer between the enzyme and electrode, and the properties often, but not inevitably, associated with enzymes, such as instability, complexity, and expense. We have now shown that the former can be overcome and that proteins can be coupled, via electrodes, to a number of energy sources; the latter is the subject of much effort elsewhere. We demonstrated previously that certain redox proteins can be reduced very efficiently electrochemically (Fig. 1a). Light and hydrogen are the two other convenient energy sources that could be used for such reductions, and we now report the reduction of cytochrome c by these means.     

彩绒革盖菌CV-8胞外酶活性研究

测定了彩绒革盖菌在PDY液体培养基中的过氧化物酶、漆酶、邻苯二酚氧化酶和意创木酚氧化酶的活性。结果发现,4种酶均有酶活性,产酶高峰也不尽相同。     

氢能或电能驱动的人工光合作用固定CO2合成糖

基于酶工程原理,通过组合自然界存在的酶促生化反应,提出自然界不存在的人工光合作用暗反应途径,只需要使用H2或电再生NADH驱动转化CO2为糖或淀粉,避开了人工光合磷酸化再生ATP难题,而且理论效率高.这种使用能源人工合成糖的方法,也是粮食生产工业化的一种潜在方法,如果将其与太阳能光伏技术或产氢技术结合,就可以实现人工光合作用,利用太阳能将CO2转换为糖.     

Mechanism of recognition of the 5' splice site in self-splicing group I introns

Group I introns include many mitochondrial ribosomal RNA and messenger RNA introns and the nuclear rRNA introns of Tetrahymena and Physarum. The splicing of precursor RNAs containing these introns is a two-step reaction. Cleavage at the 5' splice site precedes cleavage at the 3' splice site, the latter cleavage being coupled with exon ligation. Following the first cleavage, the 5' exon must somehow be held in place for ligation. We have now tested the reactivity of two self-splicing group I RNAs, the Tetrahymena pre-rRNA and the intron 1 portion of the Neurospora mitochondrial cytochrome b (cob) pre-mRNA, in the intermolecular exon ligation reaction (splicing in trans) described by Inoue et al. The different sequence specificity of the reactions supports the idea that the nucleotides immediately upstream from the 5' splice site are base-paired to an internal, 5' exon-binding site, in agreement with RNA structure models proposed by Davies and co-workers and others. The internal binding site is proposed to be involved in the formation of a structure that specifies the 5' splice site and, following the first step of splicing, to hold the 5' exon in place for exon ligation.     

Biomimetic, Catalytic Oxidation in Organic Synthesis

1 Introduction Oxidation is one of the most fundamental reactions in organic synthesis. Owing to the current need to develop forward-looking technology that is environmentally acceptable with respect many aspects. The most attractive approaches are biomimetic oxidation reactions that are closely related to the metabolism of living things. The metabolisms are governed by a variety of enzymes such as cytochrome P-450 and flavoenzyme. Simulation of the function of these enzymes with simple trans…     

Reverse self-splicing of group II intron RNAs in vitro.

Group II introns, which are classed together on the basis of a conserved secondary structure, are found in organellar genes of lower eukaryotes and plants. Like introns in nuclear pre-messenger RNA, they are excised by a two-step splicing reaction to generate branched circular RNAs, the so-called lariats. A remarkable feature of group II introns is their self-splicing activity in vitro. In the absence of a nucleotide cofactor, the intron RNAs catalyse two successive transesterification reactions which lead to autocatalytic excision of the lariat IVS from pre-mRNA and concomitantly to exon ligation. By virtue of its ability to specifically bind the 5' exon, the intron can also catalyse such reactions on exogenous RNA substrates. This sequence-specific attachment could enable group II introns to integrate into unrelated RNAs by reverse splicing, in a process similar to that described for the self-splicing Tetrahymena group I intron. Here we report that group II lariat IVS can indeed reintegrate itself into an RNA composed of the ligated exons in vitro. This occurs by a process of self-splicing that completely reverses both transesterification steps of the forward reaction: it involves a transition of the 2'-5' phosphodiester bond of the lariat RNA into the 3'-5' bond of the reconstituted 5' splice junction.     

Alteration of mouse cytochrome P450coh substrate specificity by mutation of a single amino-acid residue

As a family of structurally-related enzymes, cytochrome P450 (P450) monooxygenases exhibit paradoxical characteristics: although collectively the enzymes display a broad range of substrate specificities, individually they are characterized by a high degree of substrate and product selectivity. Mouse P45015 alpha and P450coh, for example, which are expressed in female liver and male kidney cells, catalyse 15 alpha-hydroxylation of delta 4 3-ketone steroids, such as testosterone and 7-hydroxylation of coumarin, respectively. In spite of their divergent catalytic activities, however, these enzymes differ by only 11 amino acids within their 494 residues. To determine the structural basis of the different substrate specificities of P45015 alpha and P450coh we therefore altered each of these 11 residues by site-directed mutagenesis, expressing the mutant cytochromes in COS-1 cells. We report that the activities of both cytochromes depend critically on the identities of the amino acids at positions 117, 209 and 365 and, moreover, that a single mutation in which Phe 209 is substituted by Leu is sufficient to convert the specificity of P450coh from coumarin to steroid hydroxylation.