Identifying the minimal enzymes required for anhydrotetracycline biosynthesis

The cyclohexenone ring A of tetracyclines exhibits unique structural features not observed among other aromatic polyketides. These substitutions include the C2 primary amide, C4 dimethylamine, and the C12a tertiary alcohol. Here we report the identification and reconstitution of the minimum set of enzymes required for the biosynthesis of anhydrotetracycline (ATC, 5), the first intermediate in the tetracycline biosynthetic pathway that contains the fully functionalized ring A. Using a combination of in vivo and in vitro approaches, we confirmed OxyL, OxyQ, and OxyT to be the only enzymes required to convert 6-methylpretetramid 1 into 5. OxyL is a NADPH-dependent dioxygenase that introduces two oxygen atoms into 1 to yield the unstable intermediate 4-keto-ATC 2. The aminotransferase OxyQ catalyzes the reductive amination of C4-keto of 2, yielding 4-amino-ATC 3. Furthermore, the N, N-dimethyltransferase OxyT catalyzes the formation of 5 from 3 in a (S)-adenosylmethionine (SAM)-dependent manner. Finally, a "non-natural" anhydrotetracycline derivative was generated, demonstrating that our heterologous host/vector pair can be a useful platform toward the engineered biosynthesis of tetracycline analogues.     

Formation of an aminoacyl-S-enzyme intermediate is a key step in the biosynthesis of chloramphenicol

Herein we report the first biochemical characterization of an enzyme involved in the biosynthesis of chloramphenicol that provides new insights into the origins of the antibiotic.     

Nonactin biosynthesis: the initial committed step is the condensation of acetate (malonate) and succinate

Nonactin is a macrotetrolide antibiotic produced by Streptomyces griseus subsp. griseus ETH A7796 that has shown activity against the P170-glycoprotein efflux pump associated with multiple drug resistant cancer cells. Nonactin is a polyketide, albeit a highly atypical one. The structure is composed of two units of each of the enantiomers of nonactic acid, arranged in a macrocycle, so that the molecule has S4 symmetry and is achiral. The monomer units, (+)- and (-)-nonactic acid, are derived from acetate, succinate, and propionate, although the exact details of the assembly process are quite unclear. We have used feeding experiments with a series of multiple stable isotope labeled precursors to elucidate the details of the first committed step of nonactic acid biosynthesis. We have found that the (13)C label from 3-ketoadipate is incorporated specifically into both nonactic acid and its homologue, homononactic acid. The data conclusively show that the first committed step of nonactin biosynthesis is the coupling of a succinate derivative with either acetate or malonate. The differentiation into either nonactate or homononactate occurs after the initial condensation; the homologues are not derived from use of a different "starter unit" by the nonactate polyketide synthase. The first step of nonactin biosynthesis involves achiral intermediates; differentiation between the known enantiocomplementary biosynthesis pathways to form each enantiomer of the precursor monomer units likely occurs after the initial condensation reaction.     

HIV-1 PR催化水解第3步机理的研究

在B3LYP/6-31G(d)水平下研究了HIV-1 PR催化水解反应关键性的一步,即第3步反应.模型体系包括了活化位点的3个残基,Asp25(25′)-Thr26(26′)-Gly27(27′) 主要参加反应的基团,构建了由69个原子组成的较大模型体系.进一步研究表明Thr26(26′)和Gly27(27′)在水解反应中只起到保持活化位点平面构型的作用,并未直接参与水解反应.另外,详细分析了第3步反应的分子内及分子间氢键.     

Coenzyme Q biosynthesis: Coq6 is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency

Coenzyme Q (Q), an essential component of eukaryotic cells, is synthesized by several enzymes from the?precursor 4-hydroxybenzoic acid. Mutations in six of the Q biosynthesis genes cause diseases that can sometimes be ameliorated by oral Q supplementation. We establish here that Coq6, a predicted flavin-dependent monooxygenase, is involved exclusively in the C5-hydroxylation reaction. In an unusual way, the ferredoxin Yah1 and the ferredoxin reductase Arh1 may be the in?vivo source of electrons for?Coq6. We also show that hydroxylated analogs of 4-hydroxybenzoic acid, such as vanillic acid or 3,4-dihydroxybenzoic acid, restore Q biosynthesis and respiration in a Saccharomyces cerevisiae coq6 mutant. Our results demonstrate that appropriate analogs of 4-hydroxybenzoic acid can bypass a deficient Q biosynthetic enzyme and might be considered for the treatment of some primary Q deficiencies.     

A simple approach for synthesis of hollow mesoporous nanotubes loaded with metallic and magnetic nanoparticles: Only one step is required

Hollow mesoporous polypyrrole (PPy)@Pd‐Fe₃O₄ nanotubes were prepared using MoO₃ nanorods as hard templates in one step, in which construction of PPy nanotubes, preparation of Pd nanoparticles, synthesis of Fe₃O₄ nanoparticles and removal of MoO₃ nanorods were combined together. To the best of our knowledge, this is the simplest approach for the synthesis of nanomaterials with catalytic activity, magnetic property and hollow mesoporous structure simultaneously. Although the preparation procedure was simplified, the catalytic activity and magnetic property were not sacrificed. In the catalytic reduction of 4‐nitrophenol, both reaction rate constant and turnover frequency were higher than those of previous reports. Importantly, the nanotubes could be easily separated from the reaction solution in the presence of a magnetic field, and saturation magnetization could be controlled by the amount of pyrrole monomer. After six recycles, the catalytic activity maintained 94.8% of that of the first run, indicating good stability and reusability.     

Intercalation is not required for DNA light-switch behavior

The DNA light-switch complex [Ru(bpy)2(tpphz)]2+ (1, bpy = 2,2'-bipyridine, tpphz = tetrapyrido[3,2-a:2',3'-c:3',2'-h:2',3'-j]phenazine) is luminescent when bound to DNA and in organic solvents and weakly emissive in water. To date, light-switch behavior by transition metal complexes has generally been regarded as confirmation of DNA intercalation. In contrast, the present work demonstrates that the nonintercalating bimetallic complex [(bpy)2Ru(tpphz)Ru(bpy)2]4+ (2) behaves as a DNA light-switch. Weak emission from the 3MLCT excited state of 2 is observed in water with lambda(em) = 623 nm (phi(em) = 1.4 x 10(-4)), and a red shift (lambda(em) = 702 nm) and 40-fold increase in intensity are observed upon addition of 100 microM calf thymus DNA (ct-DNA). Addition of increasing concentrations of 2 to 1 mM herring sperm DNA does not result in an increase in the viscosity of the solution, indicating that the complex is not an intercalator. Additionally, experiments were conducted to ensure that the emission enhancement did not arise from threading intercalation of the complex. The in situ generation of 2 intercalated between the base pairs of ct-DNA in a threading fashion, however, exhibits emission maximum at 685 nm, which is blue-shifted from that of surface-bound 2. DFT calculations show low-lying orbitals in 2 that are expected to exhibit nonemissive character when contributing to the MLCT state, in accord with the lower emission intensity observed for 2 relative to that for 1. To our knowledge, the present work is the first example of a nonintercalating light-switch metal complex, thus showing that light-switch behavior cannot be used exclusively as confirmation of intercalation.     

alpha-Sarcin catalytic activity is not required for cytotoxicity

Background  

α-Sarcin is a protein toxin produced by Aspergillus giganteus. It belongs to a family of cytotoxic ribonucleases that inactivate the ribosome and inhibit protein synthesis. α-Sarcin cleaves a single phosphodiester bond within the RNA backbone of the large ribosomal subunit, which makes the ribosome unrecognizable to elongation factors and, in turn, blocks protein synthesis. Although it is widely held that the protein synthesis inhibition caused by the toxin leads to cell death, it has not been directly shown that catalytically inactive mutants of α-sarcin are non-toxic when expressed directly within the cytoplasm of cells. This is important since recent studies have cast doubt on whether protein synthesis inhibition is sufficient to initiate apoptosis.     

Genome mining in streptomyces. Discovery of an unprecedented P450-catalyzed oxidative rearrangement that is the final step in the biosynthesis of pentalenolactone

The penM and pntM genes from the pentalenolactone biosynthetic gene clusters of Streptomyces exfoliatus UC5319 and Streptomyces arenae TU?469 were predicted to encode orthologous cytochrome P450s, CYP161C3 and CYP161C2, responsible for the final step in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone (1). Synthetic genes optimized for expression in Escherichia coli were used to obtain recombinant PenM and PntM, each carrying an N-terminal His(6)-tag. Both proteins showed typical reduced-CO UV maxima at 450 nm, and each bound the predicted substrate, pentalenolactone F (4), with K(D) values of 153 ± 14 and 126 ± 11 μM for PenM and PntM, respectively, as determined by UV shift titrations. PenM and PntM both catalyzed the oxidative rearrangement of 4 to 1 when incubated in the presence of NADPH, spinach ferredoxin, ferredoxin reductase, and O(2). The steady-state kinetic parameters were k(cat) = 10.5 ± 1.7 min(-1) and K(m) = 340 ± 100 μM 4 for PenM and k(cat) = 8.8 ± 0.9 min(-1) and K(m) = 430 ± 100 μM 4 for PntM. The in vivo function of both gene products was confirmed by the finding that the corresponding deletion mutants S. exfoliatus/ΔpenM ZD22 and S. arenae/ΔpntM ZD23 no longer produced pentalenolactone but accumulated the precursor pentalenolactone F. Complementation of each deletion mutant with either penM or pntM restored production of antibiotic 1. Pentalenolactone was also produced by an engineered strain of Streptomyces avermitilis that had been complemented with pntE, pntD, and either pntM or penM, as well as the S. avermitilis electron-transport genes for ferredoxin and ferrodoxin reductase, fdxD and fprD.     

Observation of an acryloyl-thiamin diphosphate adduct in the first step of clavulanic acid biosynthesis

The first committed biosynthetic step toward clavulanic acid, the clinically important beta-lactamase inhibitor, is catalyzed by the thiamin diphosphate (ThDP)-dependent enzyme N2-(2-carboxyethyl)arginine synthase (CEAS). This protein carries out a unique reaction among ThDP-dependent processes in which a C-N bond is formed, and an electrophilic acryloyl-thiazolium intermediate of ThDP is proposed to be involved, unlike the nucleophilic enamine species typically generated by this class of enzymes. Here we present evidence for the existence of the putative acryloyl adduct and report the unexpected observation of a long-wavelength chromophore (lambda = 433 nm), which we attribute to this enzyme-bound species. Chemical models were synthesized that both confirm its expected absorption (lambda = 310-320 nm) and exclude self-condensation and intramolecular imine formation with the cofactor as its cause. Circular dichroism experiments and others discount charge transfer as a likely explanation for the approximately 120 nm red shift of the chromophore ( approximately 25 kcal). Examples are well-known of charged molecules that exhibit significantly red-shifted UV-visible spectra compared to their neutral forms as, for example, polyene cations and dyes such as indigo and the cyanines. Rhodopsin is the classic biochemical example where the protein (opsin)-bound protonated Schiff base of retinal displays a remarkable range of red-shifted absorptions modulated by the protein environment. Similar tuning of the chromophoric behavior of the enzyme-bound CEAS acryloyl.ThDP species may be occurring.     

The dynamic structure of jadomycin B and the amino acid incorporation step of its biosynthesis

Jadomycin B, an antifungal antibiotic with a unique 8H-benz[b]oxazolo[3,2-f]phenanthridine pentacyclic skeleton produced by the bacterium Streptomyces venezuelae ISP 5230, exists in a dynamic equilibrium of two diastereomers differing in the configuration of C-3a. Several novel jadomycins with various amino acid-derived 1-side chains could be generated, by replacing isoleucine in the production medium of S. venezuelae with other amino acids. These two findings led to the conclusion that a nonenzymatic reaction with the amino acid followed by a likewise nonenzymatic cyclization cascade are crucial for its late biosynthesis.     

CmlI is an N-oxygenase in the biosynthesis of chloramphenicol

The N-oxygenation of an amine group is one of the steps in the biosynthesis of the antibiotic chloramphenicol. The non-heme di-iron enzyme CmlI was identified as the enzyme catalyzing this reaction through bioinformatics studies and reconstitution of enzymatic activity. In vitro reconstitution was achieved using phenazine methosulfate and NADH as electron mediators, while in vivo activity was demonstrated in Escherichia coli using two substrates. Kinetic analysis showed a biphasic behavior of the enzyme. Oxidized hydroxylamine and nitroso compounds in the reaction were detected both in vitro and in vivo based on LC–MS. The active site metal was confirmed to be iron based on a ferrozine assay. These findings provide new insights into the biosynthesis of chloramphenicol and could lead to further development of CmlI as a useful biocatalyst.     

Cucurbitadienol synthase, the first committed enzyme for cucurbitacin biosynthesis, is a distinct enzyme from cycloartenol synthase for phytosterol biosynthesis

Three oxidosqualene cyclase (OSC) cDNAs (CPX, CPQ, CPR) were cloned from seedlings of Cucurbita pepo by homology based PCR method. Their open reading frames were expressed in lanosterol synthase deficient (erg7) Saccharomyces cerevisiae strain GIL77. Analyses of in vitro enzyme activities and in vivo accumulated products in the transformants demonstrated that CPQ and CPX encode cucurbitadienol and cycloartenol synthases, respectively. These results indicated the presence of distinct OSCs for cycloartenol and cucurbitadienol synthesis in this plant.     

Phosphorylation of osteopontin is required for inhibition of calcium oxalate crystallization

Under near-physiological pH, temperature, and ionic strength, a kinetics constant composition (CC) method was used to examine the roles of phosphorylation of a 14 amino acid segment (DDVDDTDDSHQSDE) corresponding to potential crystal binding domains within the osteopontin (OPN) sequence. The phosphorylated 14-mer OPN peptide segment significantly inhibits both the nucleation and growth of calcium oxalate monohydrate (COM), inhibiting nucleation by markedly increasing induction times and delaying subsequent growth by at least 50% at concentrations less than 44 nM. Molecular modeling predicts that the doubly phosphorylated peptide binds much more strongly to both (-101) and (010) faces of COM. The estimated binding energies are, in part, consistent with the CC experimental observations. Circular dichroism spectroscopy indicates that phosphorylation does not result in conformational changes in the secondary peptide structure, suggesting that the local binding of negatively charged phosphate side chains to crystal faces controls growth inhibition. These in vitro results reveal that the interactions between phosphorylated peptide and COM crystal faces are predominantly electrostatic, further supporting the importance of macromolecules rich in anionic side chains in the inhibition of kidney stone formation. In addition, the phosphorylation-deficient form of this segment fails to inhibit COM crystal growth up to concentrations of 1450 nM. However, at sufficiently high concentrations, this nonphosphorylated segment promotes COM nucleation. Dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) results confirm that aggregation of the nonphosphorylated peptide segment takes place in solution above 900 nM when the aggregated peptide particles may exceed a well-defined minimum size to be effective crystallization promoters.     

Light-induced charge redistribution in the retinal chromophore is required for initiating the bacteriorhodopsin photocycle

Bacteriorhodopsin's photocycle is initiated by the retinal chromophore light absorption. It has usually been assumed that light primarily isomerizes a retinal double bond which in turn induces protein conformational alterations and biological activity. We have studied several artificial pigments derived from retinal analogues tailored to substantially reduce the light-induced chromophore polarization. The lack of chromophore polarization was reflected in an undetectable second harmonic generation (SHG) signal. It was revealed that these artificial pigments did not exhibit any detectable light-induced photocycle nor light acceleration of the hydroxylamine-bleaching reaction. We suggest that light-induced retinal polarization triggers protein polarization which controls the course of the isomerization reaction by determining the relative efficiency of forward versus back-branching processes.     

Spreading fully at the ice-water interface is required for high ice recrystallization inhibition activity

Although materials for ice recrystallization inhibition(IRI) are essential for the cryopreservation of cells and tissues, there exists no guiding mechanism for the design of such materials. Therefore, the construction of materials for IRI relies on the try-and-error strategy. Herein, through changing the tacticity of hydroxyl groups on poly(vinyl alcohol)(PVA) backbones with the affinities of PVAs to ice unchanged, we experimentally find IRI activity decreases significantly for isotactic PVA in comparison to that of atactic PVA. Molecular dynamics simulation shows atactic PVA spreads fully at the ice-water interface due to its much stronger interaction with water. This indicates atactic PVA can cover more ice surface and possess a higher IRI activity when the same amount of PVAs are used, which is consistent with the results that PVA can cover the same amount of ice surface more efficiently through experimentally measuring the adsorption of PVAs on the ice surface. A guiding mechanism of high active IRI materials can be obtained: only having affinity to ice is not enough to obtain high IRI activity(i.e., only small amount of materials is required to reduce the size of ice crystals to ca.(35±10) μm), IRI agents must also have high affinity to water, i.e., low interfacial energies, to both ice and water. The former is to guarantee the adsorption of the IRI agent on the ice surface, and the latter is required for the IRI agent to spread sufficiently at the ice-water interface. Therefore, each IRI molecule can effectively block the diffusion of water onto the ice surface, and consequently inhibits the growth of ice. A spreading coefficient of IRI agents is therefore introduced to quantitatively assess the capability of IRI agents to spread at the ice-water interface.     

Glucose is required to maintain high ATP-levels for the energy-utilizing steps during PDT-induced apoptosis

Photodynamic therapy (PDT) may trigger apoptosis or necrosis in cancer cells. Several steps in the induction and execution of apoptosis require high amounts of adenosine-5'-triphosphate (ATP). Because the mitochondrial membrane potential (delta psi) decreases early in apoptosis, we raised the question about the mechanisms of maintaining a sufficiently high ATP level. We therefore monitored delta psi and the intracellular ATP level of apoptotic human epidermoid carcinoma cells (A431) after photodynamic treatment with aluminum (III) phthalocyanine tetrasulfonate. A maximum of caspase-3-like activity and nuclear fragmentation was found at fluences of about 4 J cm(-2). Under these conditions apoptotic cells reduced delta psi rapidly, while the ATP level remained high for 4-6 h after treatment for cells supplied with glucose. To analyze the contribution of glycolysis to the energy supply during apoptosis, experiments were carried out with cells deprived of glucose. These cells showed a rapid drop of ATP content and neither caspase activation nor nuclear fragmentation could be detected. We conclude that the use of glucose as a source of ATP is obligatory for the execution of PDT-induced apoptosis.