A global two component signal transduction system that integrates the control of photosynthesis, carbon dioxide assimilation, and nitrogen fixation

Photosynthesis, biological nitrogen fixation, and carbon dioxide assimilation are three fundamental biological processes catalyzed by photosynthetic bacteria. In the present study, it is shown that mutant strains of the nonsulfur purple photosynthetic bacteria Rhodospirillum rubrum and Rhodobacter sphaeroides, containing a blockage in the primary CO2 assimilatory pathway, derepress the synthesis of components of the nitrogen fixation enzyme complex and abrogate normal control mechanisms. The absence of the Calvin–Benson–Bassham (CBB) reductive pentose phosphate CO2 fixation pathway removes an important route for the dissipation of excess reducing power. Thus, the mutant strains develop alternative means to remove these reducing equivalents, resulting in the synthesis of large amounts of nitrogenase even in the presence of ammonia. This response is under the control of a global two-component signal transduction system previously found to regulate photosystem biosynthesis and the transcription of genes required for CO2 fixation through the CBB pathway and alternative routes. In addition, this two-component system directly controls the ability of these bacteria to grow under nitrogen-fixing conditions. These results indicate that there is a molecular link between the CBB and nitrogen fixation process, allowing the cell to overcome powerful control mechanisms to remove excess reducing power generated by photosynthesis and carbon metabolism. Furthermore, these results suggest that the two-component system integrates the expression of genes required for the three processes of photosynthesis, nitrogen fixation, and carbon dioxide fixation.

Yeast flavin-containing monooxygenase is induced by the unfolded protein response

Flavin-containing monooxygenase from yeast (yFMO) carries out the O2- and NADPH-dependent oxidation of biological thiols, including oxidizing glutathione to glutathione disulfide. FMO provides a large fraction of the oxidizing necessary for proper folding of disulfide bond-containing proteins; deletion of the enzyme reduces proper folding of endogenous carboxypeptidase Y by about 40%. The enzyme is not essential to cell viability because other enzymes can generate a significant fraction of the oxidizing equivalents required by the cell. However, yFMO is vital to the yeast response to reductive stress. FMO1 deletion mutants grow poorly under reductive stress, and carboxypeptidase Y activity is less than 10% of that in a stressed wild type. The FMO1 gene appears to be under control of an unfolded protein response element and is inducible by factors, such as reductive stress, that elicit the unfolded protein response. Reductive stress can increase yFMO activity at least 6-fold. This increased activity allows the cell to process endogenous disulfide bond-containing proteins and also to allow correct folding of disulfide-bonded proteins expressed from multicopy plasmids. The unfolded protein response is mediated by the Hac1p transcription factor that mediates virtually all of the induction of yFMO triggered by exogenous reducing agents.

Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods

A novel protein superfamily with over 600 members was discovered by iterative profile searches and analyzed with powerful bioinformatics and information visualization methods. Evidence exists that these proteins generate a radical species by reductive cleavage of S-adenosylmethionine (SAM) through an unusual Fe-S center. The superfamily (named here Radical SAM) provides evidence that radical-based catalysis is important in a number of previously well- studied but unresolved biochemical pathways and reflects an ancient conserved mechanistic approach to difficult chemistries. Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulfur insertion, ring formation, anaerobic oxidation and protein radical formation. They function in DNA precursor, vitamin, cofactor, antibiotic and herbicide biosynthesis and in biodegradation pathways. One eukaryotic member is interferon-inducible and is considered a candidate drug target for osteoporosis; another is observed to bind the neuronal Cdk5 activator protein. Five defining members not previously recognized as homologs are lysine 2,3-aminomutase, biotin synthase, lipoic acid synthase and the activating enzymes for pyruvate formate-lyase and anaerobic ribonucleotide reductase. Two functional predictions for unknown proteins are made based on integrating other data types such as motif, domain, operon and biochemical pathway into an organized view of similarity relationships.

Participation of Mitochondrial Metabolism in Photorespiration1 : Reconstituted System of Peroxisomes and Mitochondria from Spinach Leaves

In this study the interplay of mitochondria and peroxisomes in photorespiration was simulated in a reconstituted system of isolated mitochondria and peroxisomes from spinach (Spinacia oleracea L.) leaves. The mitochondria oxidizing glycine produced serine, which was reduced in the peroxisomes to glycerate. The required reducing equivalents were provided by the mitochondria via the malate-oxaloacetate (OAA) shuttle, in which OAA was reduced in the mitochondrial matrix by NADH generated during glycine oxidation. The rate of peroxisomal glycerate formation, as compared with peroxisomal protein, resembled the corresponding rate required during leaf photosynthesis under ambient conditions. When the reconstituted system produced glycerate at this rate, the malate-to-OAA ratio was in equilibrium with a ratio of NADH/NAD of 8.8 × 10−3. This low ratio is in the same range as the ratio of NADH/NAD in the cytosol of mesophyll cells of intact illuminated spinach leaves, as we had estimated earlier. This result demonstrates that in the photorespiratory cycle a transfer of redox equivalents from the mitochondria to peroxisomes, as postulated from separate experiments with isolated mitochondria and peroxisomes, can indeed operate under conditions of the very low reductive state of the NADH/NAD system prevailing in the cytosol of mesophyll cells in a leaf during photosynthesis.

The cellulose-binding domain of the major cellobiohydrolase of Trichoderma reesei exhibits true reversibility and a high exchange rate on crystalline cellulose.

Cellulose-binding domains (CBDs) bind specifically to cellulose, and form distinct domains of most cellulose degrading enzymes. The CBD-mediated binding of the enzyme has a fundamental role in the hydrolysis of the solid cellulose substrate. In this work we have investigated the reversibility and kinetics of the binding of the CBD from Trichoderma reesei cellobiohydrolase I on microcrystalline cellulose. The CBD was produced in Escherichia coli, purified, and radioactively labeled by reductive alkylation with 3H. Sensitive detection of the labeled CBD allowed more detailed analysis of its behavior than has been possible before, and important novel features were resolved. Binding of the CBD was found to be temperature sensitive, with an increased affinity at lower temperatures. The interaction of the CBD with cellulose was shown to be fully reversible and the CBD could be eluted from cellulose by simple dilution. The rate of exchange measured for the CBD-cellulose interaction compares well with the hydrolysis rate of cellobiohydrolase I, which is consistent with its proposed mode of action as a processive exoglucanase.

Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.

D-amino acid oxidase is the prototype of the FAD-dependent oxidases. It catalyses the oxidation of D-amino acids to the corresponding alpha-ketoacids. The reducing equivalents are transferred to molecular oxygen with production of hydrogen peroxide. We have solved the crystal structure of the complex of D-amino acid oxidase with benzoate, a competitive inhibitor of the substrate, by single isomorphous replacement and eightfold averaging. Each monomer is formed by two domains with an overall topology similar to that of p-hydroxybenzoate hydroxylase. The benzoate molecule lays parallel to the flavin ring and is held in position by a salt bridge with Arg-283. Analysis of the active site shows that no side chains are properly positioned to act as the postulated base required for the catalytic carboanion mechanism. On the contrary, the benzoate binding mode suggests a direct transfer of the substrate alpha-hydrogen to the flavin during the enzyme reductive half-reaction.The active site Of D-amino acid oxidase exhibits a striking similarity with that of flavocytochrome b2, a structurally unrelated FMN-dependent flavoenzyme. The active site groups (if these two enzymes are in fact superimposable once the mirror-image of the flavocytochrome b2 active site is generated with respect to the flavin plane. Therefore, the catalytic sites of D-amino acid oxidase and flavocytochrome b2 appear to have converged to a highly similar but enantiomeric architecture in order to catalvze similar reactions (oxidation of alpha-amino acids or alpha-hydroxy acids), although with opposite stereochemistry.

Thiocalsin: a thioredoxin-linked, substrate-specific protease dependent on calcium.

We describe a protease, named "thiocalsin," that is activated by calcium but only after reductive activation by thioredoxin, a small protein with a redox-active disulfide group that functions widely in regulation. Thiocalsin appeared to be a 14-kDa serine protease that functions independently of calmodulin. The enzyme, purified from germinating wheat grain, specifically cleaved the major indigenous storage proteins, gliadins and glutenins, after they too had been reduced, preferentially by thioredoxin. The disulfide groups of the enzyme, as well as its protein substrates, were reduced by thioredoxin via NADPH and the associated enzyme, NADP-thioredoxin reductase. The results broaden the roles of thioredoxin and calcium and suggest a joint function in activating thiocalsin, thereby providing amino acids for germination and seedling development.

The peptide binding site of the substance P (NK-1) receptor localized by a photoreactive analogue of substance P: presence of a disulfide bond.

Substance P (SP) is a neuropeptide that mediates multiple physiological responses including transmission of painful stimuli and inflammation via an interaction with a receptor of known primary sequence. To identify the regions of the SP receptor, also termed the NK-1 receptor, involved in peptide recognition, we are using analogues of SP containing the photoreactive amino acid p-benzoyl-L-phenylalanine (Bpa). In the present study, we used radioiodinated Bpa8-SP to covalently label with high efficiency the rat SP receptor expressed in a transfected mammalian cell line. To identify the amino acid residue that serves as the site of covalent attachment, a membrane preparation of labeled receptor was subjected to partial enzymatic cleavage by trypsin. A major digestion product of 22 kDa was identified. Upon reduction with 2-mercaptoethanol the mass of this product decreased to 14 kDa. The 22-kDa tryptic fragment was purified in excellent yield by preparative SDS/PAGE under nonreducing conditions. Subcleavage with Staphylococcus aureus V8 protease and endoproteinase ArgC yielded fragments of 8.2 and 9.0 kDa, respectively. Upon reductive cleavage, the V8 protease fragment decreased to 3.0 kDa while the endoproteinase ArgC fragment decreased to 3.2 kDa. Taking into consideration enzyme specificity, molecular size, determination of the presence or absence of N-glycosylation sites, and recognition by antibodies to specific sequences of the SP receptor, the V8 protease fragment is Thr-173 to Glu-183, while the endoproteinase ArgC fragment is Val-178 to Arg-190. These two fragments share the common sequence Val-Val-Cys-Met-Ile-Glu (residues 178-183). The site of covalent attachment of radioiodinated Bpa8-SP is thus restricted to a residue within this overlap sequence. The data presented here also establish that the cysteine residue in this sequence Cys-180, which is positioned in the middle of the second extracellular loop, participates in a disulfide bond that links the first and second extracellular loops of the receptor.

Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent.

An autotrophic theory of the origin of metabolism and life has been proposed in which carbon dioxide is reduced by ferrous sulfide and hydrogen sulfide by means of a reversed citric acid cycle, leading to the production of amino acids. Similar processes have been proposed for purine synthesis. Ferrous sulfide is a strong reducing agent in the presence of hydrogen sulfide and can produce hydrogen as well as reduce alkenes, alkynes, and thiols to saturated hydrocarbons and reduce ketones to thiols. However, the reduction of carbon dioxide has not been demonstrated. We show here that no amino acids, purines, or pyrimidines are produced from carbon dioxide with the ferrous sulfide and hydrogen sulfide system. Furthermore, this system does not produce amino acids from carboxylic acids by reductive amination and carboxylation. Thus, the proposed autotrophic theory, using carbon dioxide, ferrous sulfide, and hydrogen sulfide, lacks the robustness needed to be a geological process and is, therefore, unlikely to have played a role in the origin of metabolism or the origin of life.

The three-dimensional structure of NAD(P)H:quinone reductase, a flavoprotein involved in cancer chemoprotection and chemotherapy: mechanism of the two-electron reduction.

Quinone reductase [NAD(P)H:(quinone acceptor) oxidoreductase, EC 1.6.99.2], also called DT diaphorase, is a homodimeric FAD-containing enzyme that catalyzes obligatory NAD(P)H-dependent two-electron reductions of quinones and protects cells against the toxic and neoplastic effects of free radicals and reactive oxygen species arising from one-electron reductions. These two-electron reductions participate in the reductive bioactivation of cancer chemotherapeutic agents such as mitomycin C in tumor cells. Thus, surprisingly, the same enzymatic reaction that protects normal cells activates cytotoxic drugs used in cancer chemotherapy. The 2.1-A crystal structure of rat liver quinone reductase reveals that the folding of a portion of each monomer is similar to that of flavodoxin, a bacterial FMN-containing protein. Two additional portions of the polypeptide chains are involved in dimerization and in formation of the two identical catalytic sites to which both monomers contribute. The crystallographic structures of two FAD-containing enzyme complexes (one containing NADP+, the other containing duroquinone) suggest that direct hydride transfers from NAD(P)H to FAD and from FADH2 to the quinone [which occupies the site vacated by NAD(P)H] provide a simple rationale for the obligatory two-electron reductions involving a ping-pong mechanism.

Inactivation of ethanol-inducible cytochrome P450 and other microsomal P450 isozymes by trans-4-hydroxy-2-nonenal, a major product of membrane lipid peroxidation.

Of the microsomal P450 cytochromes, the ethanol-inducible isoform, P450 2E1, is believed to be predominant in leading to oxidative damage, including the generation of radical species that contribute to lipid peroxidation, and in the reductive beta-scission of lipid hydroperoxides to give hydrocarbons and aldehydes. In the present study, the sensitivity of a series of P450s to trans-4-hydroxy-2-nonenal (HNE), a known toxic product of membrane lipid peroxidation, was determined. After incubation of a purified cytochrome with HNE, the other components of the reconstituted system (NADPH-cytochrome P450 reductase, phosphatidylcholine, and NADPH) were added, and the rate of oxygenation of 1-phenylethanol to yield acetophenone was assayed. Inactivation occurs in a time-dependent and HNE concentration-dependent manner, with P450s 2E1 and 1A1 being the most sensitive, followed by isoforms 1A2, 3A6, and 2B4. At an HNE concentration of 0.24 microM, which was close to the micromolar concentration of the enzyme, four of the isoforms were significantly inhibited, but not P450 2B4. In other experiments, the reductase was shown to be only relatively weakly inactivated by HNE. P450s 2E1 and 2B4 in microsomal membranes from animals induced with acetone or phenobarbital, respectively, are as readily inhibited as the purified forms. Evidence was obtained that the P450 heme is apparently not altered and the sulfur ligand is not displaced, that substrate protects against HNE, and that the inactivation is reversed upon dialysis. Higher levels of reductase or substrate do not restore the activity of inhibited P450 in the catalytic assay. Our results suggest that the observed inhibition of the various P450s is of sufficient magnitude to cause significant changes in the metabolism of foreign compounds such as drugs and chemical carcinogens by the P450 oxygenase system at HNE concentrations that occur in biological membranes. In view of the known activities of P450 2E1 in generating lipid hydroperoxides and in their beta-scission, its inhibition by this product of membrane peroxidation may provide a negative regulatory function.

Análise dos parâmetros que interferem no metabolismo da microbiota anaeróbia e anóxica na remoção de bifenilas policloradas

A elevada concentração de cloro das bifenilas policloradas provoca alta toxicidade do composto, o qual dificulta sua biodegradação. A contaminação de PCB no Brasil foi confirmada em estudo realizado na Bahia de Santos-São Vicente (São Paulo), o qual revelou a necessidade de um plano de ação para o controle e remoção de PCB no Brasil. Pretendeu-se assim, na realização da presente pesquisa, verificar quatro hipóteses: (1) A técnica de Microextração em fase sólida é uma metodologia eficaz para avaliação de bifenilas policloradas de amostras de reatores; (2) A condição fermentativa-metanogênica abriga comunidade resistente ao PCB, e removê-lo; (3) A condição desnitrificante abriga comunidade resistente ao PCB, e removê-lo e (4) A remoção de PCB, bem como, a composição microbiana é distinta em cada condição metabólica. Para tanto, reatores em batelada foram montados separadamente com biomassa anaeróbia proveniente de reator UASB usado no tratamento de água residuária de avicultura e biomassa de sistemas de lodos ativados de tratamento de esgoto sanitário. Os reatores operados em condição mesófila foram alimentados com meio sintético, co-substratos, sendo etanol (457 mg.L-1) e formiato de sódio (680 mg.L-1) para os reatores anaeróbios, e somente etanol (598 mg.L-1) para os reatores anóxicos, além de PCB padrão Sigma (congêneres PCBs 10, 28, 52, 153, 138 e 180) em diferentes concentrações, dependendo do objetivo do ensaio. A aplicação do método de extração por SPME com análise em cromatógrafo gasoso com detector por captura de elétrons foi adequada para a determinação dos seis congêneres de PCB. Obteve-se ampla faixa de linearidade, seletividade frente aos vários interferentes, além da robustez do método, utilidade e confiabilidade na identificação e quantificação específica dos seis congêneres de PCB. A Hipótese 1 foi aceita; ou seja, por meio da aplicação da metodologia SPME foi possível quantificar os PCB nos reatores em batelada. Apesar de ter sido comprovada a inibição metanogênica na presença de PCB, com IC50 de 0,03 mg.L

Detritylation of Protected Tetrazoles by Naphthalene-Catalyzed Lithiation

Treatment of N-tritylated tetrazoles bearing aliphatic, aromatic, or heteroaromatic substituents (including functionalized ones) with lithium powder and a catalytic amount of naphthalene led to reductive removal of the trityl group to give excellent yields of the corresponding free tetrazoles without decomposition of the tetrazole ring. The detritylation process was successfully extended to several tetrazoles that are components of sartans, an interesting class of drugs. The chemoselectivity between trityl–tetrazole and trityl­–amine bond-cleavage reactions was also studied. This method represents an efficient technique for deprotection of tritylated tetrazoles under non-acidic conditions.

Sm-Nd isotope and Mn/Ca ratios for cleaned Neogloboquadrina pachyderma from ODP Hole 105-647A (Table 1)

The neodymium (Nd) isotope composition of ancient seawater is a potentially useful tracer of changes in continental inputs and ocean circulation on timescales of a few ka. Here we present the first Nd isotope record for seawater using sedimentary foraminifera cleaned using standard oxidative-reductive techniques. The data, along with Mn/Ca ratios, suggest that cleaned foraminifera provide a reliable record of Nd in seawater and hold out the prospect of using Nd in foraminifera to examine changes in seawater that accompany glacial-interglacial climatic cycles. The principal potential problem to be overcome with the use of forams as records of trace elements in ancient seawater is their diagenetic Fe-Mn coatings. These contain large amounts of Nd and other trace elements but can be cleaned off using highly reducing reagents. Mn(Ca ratios for the majority of the cleaned sedimentary foraminifera analysed here lie within the range (10-100 µmol/mol) that has yielded success in studies of transition elements in forams. Mass-balance modelling suggests that for residual Mn/Ca ratios <100 µmol/mol, Nd added to the foram in the coating will never shift the measured Nd isotope composition significantly away from the seawater value acquired by the foram test in the water column. Additionally, Nd concentrations measured in cleaned sedimentary foraminifera are comparable with those for a modern sample that has never encountered diagenetic fluids. Finally, core-top planktonic foraminifera for two sites have Nd isotope compositions that are identical to local surface seawater. The data we present here for Labrador Sea forams over the past 2.5 m.y. are interpreted in terms of changes in the seawater isotopic composition. The data show a pronounced shift from epsilon-Nd values of ~-12 to ~-19 in the period 2.5-1.5 Ma. This change is interpreted to result from the initiation of Northern Hemisphere glaciation and the increased derivation of Labrador Sea Nd via ice-rafting from Archaean terranes in central Canada. In combination with stable isotope and foraminiferal relative species abundance data, the new Nd data are consistent with the surface hydrography of the Labrador Sea being dominated by a fluctuating balance between cold, polar waters containing unradiogenic Nd and warm, subtropical waters containing more radiogenic Nd. The major change in Labrador Sea Nd that is observed in the past 2.5 Ma can, on its own, account for the change in the Nd isotope composition of North Atlantic Deep Water over the same time period.

Rhenium and osmium concentrations and isotopic compositions in altered ocean crust rocks at ODP Site 185-801

Re and Os concentrations and Os isotopic ratios were determined for composite samples prepared from volcanoclastics (VCL) and basaltic flows (FLO) from Jurassic oceanic crust (Ocean Drilling Program Leg 185, Site 801 in the western Pacific), with the aim of determining the effect of seafloor weathering on the Re-Os budget. A supercomposite sample, prepared from a proportionate mixture of the various composite powders, served to represent the average composition of the altered oceanic crust [Kelley, K.A., Plank, T., Ludden, J. and Staudigel, H., (2003). Composition of altered oceanic crust at ODP Sites 801 and 1149, Geochem. Geophys. Geosyst. 4(6) 8910, doi:10.1029/2002GC000435.]. Re contents vary from 0.2 to 1.3 ng/g, and from 2.2 to 3.1 ng/g in the VCL and FLO composites respectively. Os contents vary from 0.005 to 0.047 ng/g in the VCL, and from 0.008 to 0.027 ng/g in the FLO composites. The FLO composites have much higher Re/Os ratios and thus have more radiogenic Os compositions (187Os/188Os = 1.38 to 8.48) than the VCL composites (187Os/188Os = 0.32 to 4.40). The VCL composite from the upper section of the crust shows evidence for substantial Re loss and Os uptake, consistent with oxidative weathering processes. However, Re uptake during weathering processes under more reducing conditions, evident in the FLO samples from throughout the section and to a lesser extent in the lower VCL samples, more than compensates for this Re loss in the upper VCL. Os concentrations were essentially unchanged by these reductive processes. Model age calculations suggest that Re uptake continued for tens of millions of years after crust formation. Abundant secondary pyrite is found throughout the altered Hole 801C crust in zones of restricted seawater flow, and this may have accommodated an important part of the input Re. The Re content of the supercomposite (~2.2 ng/g) is about 1 ng/g higher than would be expected on the basis of its Yb content. If the results from Hole 801C are typical, they suggest that the Re concentration of at least the upper part of the oceanic crust may be nearly doubled during seafloor alteration. Such large extents of Re uptake would have a significant effect on the oceanic Re budget. Furthermore, assuming that they survive passage through the subduction zone, these elevated Re contents would greatly decrease the proportion of subducted oceanic crust required in the source region to explain the radiogenic Os compositions of many ocean island basalts.