@article {3086, title = {Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H and CO compared to organotrophic growth with fructose.}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 Oct 13}, pages = {13135}, abstract = {

Clostridium ljungdahlii derives energy by lithotrophic and organotrophic acetogenesis. C. ljungdahlii was grown organotrophically with fructose and also lithotrophically, either with syngas - a gas mixture containing hydrogen (H), carbon dioxide (CO), and carbon monoxide (CO), or with H and CO. Gene expression was compared quantitatively by microarrays using RNA extracted from all three conditions. Gene expression with fructose and with H/CO was compared by RNA-Seq. Upregulated genes with both syngas and H/CO (compared to fructose) point to the urea cycle, uptake and degradation of peptides and amino acids, response to sulfur starvation, potentially NADPH-producing pathways involving (S)-malate and ornithine, quorum sensing, sporulation, and cell wall remodeling, suggesting a global and multicellular response to lithotrophic conditions. With syngas, the upregulated (R)-lactate dehydrogenase gene represents a route of electron transfer from ferredoxin to NAD. With H/CO, flavodoxin and histidine biosynthesis genes were upregulated. Downregulated genes corresponded to an intracytoplasmic microcompartment for disposal of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several cytoplasmic and membrane-associated redox-active protein genes were differentially regulated. The transcriptomic profiles of C. ljungdahlii in lithotrophic and organotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide biofuel and commodity chemical production with this species.

}, keywords = {Carbon Dioxide, Carbon Monoxide, Clostridium, Fructose, Hydrogen, NADP, Transcriptome}, issn = {2045-2322}, doi = {10.1038/s41598-017-12712-w}, author = {Aklujkar, Muktak and Leang, Ching and Shrestha, Pravin M and Shrestha, Minita and Lovley, Derek R} } @article {476, title = {Geobacter sulfurreducens strain engineered for increased rates of respiration.}, journal = {Metab Eng}, volume = {10}, year = {2008}, month = {2008 Sep}, pages = {267-75}, abstract = {Geobacter species are among the most effective microorganisms known for the bioremediation of radioactive and toxic metals in contaminated subsurface environments and for converting organic compounds to electricity in microbial fuel cells. However, faster rates of electron transfer could aid in optimizing these processes. Therefore, the Optknock strain design methodology was applied in an iterative manner to the constraint-based, in silico model of Geobacter sulfurreducens to identify gene deletions predicted to increase respiration rates. The common factor in the Optknock predictions was that each resulted in a predicted increase in the cellular ATP demand, either by creating ATP-consuming futile cycles or decreasing the availability of reducing equivalents and inorganic phosphate for ATP biosynthesis. The in silico model predicted that increasing the ATP demand would result in higher fluxes of acetate through the TCA cycle and higher rates of NADPH oxidation coupled with decreases in flux in reactions that funnel acetate toward biosynthetic pathways. A strain of G. sulfurreducens was constructed in which the hydrolytic, F(1) portion of the membrane-bound F(0)F(1) (H(+))-ATP synthase complex was expressed when IPTG was added to the medium. Induction of the ATP drain decreased the ATP content of the cell by more than half. The cells with the ATP drain had higher rates of respiration, slower growth rates, and a lower cell yield. Genome-wide analysis of gene transcript levels indicated that when the higher rate of respiration was induced transcript levels were higher for genes involved in energy metabolism, especially in those encoding TCA cycle enzymes, subunits of the NADH dehydrogenase, and proteins involved in electron acceptor reduction. This was accompanied by lower transcript levels for genes encoding proteins involved in amino acid biosynthesis, cell growth, and motility. Several changes in gene expression that involve processes not included in the in silico model were also detected, including increased expression of a number of redox-active proteins, such as c-type cytochromes and a putative multicopper outer-surface protein. The results demonstrate that it is possible to genetically engineer increased respiration rates in G. sulfurreducens in accordance with predictions from in silico metabolic modeling. To our knowledge, this is the first report of metabolic engineering to increase the respiratory rate of a microorganism.}, keywords = {Adenosine Triphosphate, Bacterial Proteins, Biodegradation, Environmental, Citric Acid Cycle, Electron Transport, Geobacter, Metals, Models, Biological, NADH Dehydrogenase, NADP, Oxygen Consumption, Phosphates, Proton-Translocating ATPases, Radioactive Pollutants}, issn = {1096-7184}, doi = {10.1016/j.ymben.2008.06.005}, author = {Izallalen, Mounir and Mahadevan, Radhakrishnan and Burgard, Anthony and Postier, Bradley and DiDonato, Raymond and Sun, Jun and Schilling, Christopher H and Lovley, Derek R} } @article {1212, title = {Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum.}, journal = {Extremophiles}, volume = {11}, year = {2007}, month = {2007 Sep}, pages = {741-6}, abstract = {

Native and recombinant malate dehydrogenase (MDH) was characterized from the hyperthermophilic, facultatively autotrophic archaeon Pyrobaculum islandicum. The enzyme is a homotetramer with a subunit mass of 33 kDa. The activity kinetics of the native and recombinant proteins are the same. The apparent K ( m ) values of the recombinant protein for oxaloacetate (OAA) and NADH (at 80 degrees C and pH 8.0) were 15 and 86 microM, respectively, with specific activity as high as 470 U mg(-1). Activity decreased more than 90\% when NADPH was used. The catalytic efficiency of OAA reduction by P. islandicum MDH using NADH was significantly higher than that reported for any other archaeal MDH. Unlike other archaeal MDHs, specific activity of the P. islandicum MDH back-reaction also decreased more than 90\% when malate and NAD(+) were used as substrates and was not detected with NADP(+). A phylogenetic tree of 31 archaeal MDHs shows that they fall into 5 distinct groups separated largely along taxonomic lines suggesting minimal lateral mdh transfer between Archaea.

}, keywords = {Citric Acid Cycle, Hydrogen-Ion Concentration, Kinetics, Malate Dehydrogenase, Malates, Molecular Weight, NAD, NADP, Oxaloacetic Acid, Phylogeny, Protein Conformation, Protein Subunits, Pyrobaculum, Recombinant Proteins, Sequence Analysis, Protein, Substrate Specificity, Temperature}, issn = {1431-0651}, doi = {10.1007/s00792-007-0081-2}, author = {Yennaco, Lynda J and Hu, Yajing and Holden, James F} } @article {606, title = {Differences in Fe(III) reduction in the hyperthermophilic archaeon, Pyrobaculum islandicum, versus mesophilic Fe(III)-reducing bacteria.}, journal = {FEMS Microbiol Lett}, volume = {195}, year = {2001}, month = {2001 Feb 20}, pages = {253-8}, abstract = {The discovery that all hyperthermophiles that have been evaluated have the capacity to reduce Fe(III) has raised the question of whether mechanisms for dissimilatory Fe(III) reduction have been conserved throughout microbial evolution. Many studies have suggested that c-type cytochromes are integral components in electron transport to Fe(III) in mesophilic dissimilatory Fe(III)-reducing microorganisms. However, Pyrobaculum islandicum, the hyperthermophile in which Fe(III) reduction has been most intensively studied, did not contain c-type cytochromes. NADPH was a better electron donor for the Fe(III) reductase activity in P. islandicum than NADH. This is the opposite of what has been observed with mesophiles. Thus, if previous models for dissimilatory Fe(III) reduction by mesophilic bacteria are correct, then it is unlikely that a single strategy for electron transport to Fe(III) is present in all dissimilatory Fe(III)-reducing microorganisms.}, keywords = {Cytochrome c Group, Electron Transport, Ferric Compounds, FMN Reductase, NADH, NADPH Oxidoreductases, NADP, Oxidation-Reduction, Temperature, Thermoproteaceae}, issn = {0378-1097}, author = {Childers, S E and Lovley, D R} } @article {592, title = {Isolation and characterization of a soluble NADPH-dependent Fe(III) reductase from Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {183}, year = {2001}, month = {2001 Aug}, pages = {4468-76}, abstract = {NADPH is an intermediate in the oxidation of organic compounds coupled to Fe(III) reduction in Geobacter species, but Fe(III) reduction with NADPH as the electron donor has not been studied in these organisms. Crude extracts of Geobacter sulfurreducens catalyzed the NADPH-dependent reduction of Fe(III)-nitrilotriacetic acid (NTA). The responsible enzyme, which was recovered in the soluble protein fraction, was purified to apparent homogeneity in a four-step procedure. Its specific activity for Fe(III) reduction was 65 micromol. min(-1). mg(-1). The soluble Fe(III) reductase was specific for NADPH and did not utilize NADH as an electron donor. Although the enzyme reduced several forms of Fe(III), Fe(III)-NTA was the preferred electron acceptor. The protein possessed methyl viologen:NADP(+) oxidoreductase activity and catalyzed the reduction of NADP(+) with reduced methyl viologen as electron donor at a rate of 385 U/mg. The enzyme consisted of two subunits with molecular masses of 87 and 78 kDa and had a native molecular mass of 320 kDa, as determined by gel filtration. The purified enzyme contained 28.9 mol of Fe, 17.4 mol of acid-labile sulfur, and 0.7 mol of flavin adenine dinucleotide per mol of protein. The genes encoding the two subunits were identified in the complete sequence of the G. sulfurreducens genome from the N-terminal amino acid sequences derived from the subunits of the purified protein. The sequences of the two subunits had about 30\% amino acid identity to the respective subunits of the formate dehydrogenase from Moorella thermoacetica, but the soluble Fe(III) reductase did not possess formate dehydrogenase activity. This soluble Fe(III) reductase differs significantly from previously characterized dissimilatory and assimilatory Fe(III) reductases in its molecular composition and cofactor content.}, keywords = {Amino Acid Sequence, Bacterial Proteins, Deltaproteobacteria, Ferric Compounds, FMN Reductase, Molecular Sequence Data, NADH, NADPH Oxidoreductases, NADP, Nitrilotriacetic Acid, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Solubility}, issn = {0021-9193}, doi = {10.1128/JB.183.15.4468-4476.2001}, author = {Kaufmann, F and Lovley, D R} } @article {1739, title = {Bacterial metabolism of resorcinylic compounds: purification and properties of orcinol hydroxylase and resorcinol hydroxylase from Pseudomonas putida ORC.}, journal = {Eur J Biochem}, volume = {61}, year = {1976}, month = {1976 Jan 2}, pages = {259-69}, abstract = {

The hydroxylase activities observed in extracts of Pseudomonas putida ORC after growth on orcinol and resorcinol as sole source of carbon have been purified to homogeneity. Both enzymes were shown to be flavoproteins and to contain approximately 1 mol of FAD for each polypeptide chain, S20,W values for each enzyme are 4.1 +/- 0.1 and are independent of the presence of their aromatic substrates. Molecular weight determinations under native (approximately 68000) and denaturing (approximately 70000) conditions indicated that they are monomeric. The visible absorption spectra identical but the circular dichroic spectra of the two proteins can be distinguished. Although each protein catalyzes the NAD(P)H and O2-dependent hydroxylation of both orcinol and resorcinol, the efficiency of the transformations of the substrates by the two enzymes is radically different; furthermore resorcinol hydroxylase is much more versatile in the aromatic compounds it can utilize as substrates and effectors. Other properties of the enzymes which clearly establish their own identity include their serological characteristics and amino acid composition; the latter property is particularly evident when the quantities of valine and alanine residues are compared. The synthesis of each enzyme is also under different regulatory constraints, being controlled by the substrate used for growth.

}, keywords = {Amino Acids, Circular Dichroism, Flavin-Adenine Dinucleotide, Mixed Function Oxygenases, Molecular Weight, NAD, NADP, Oxidation-Reduction, Protein Conformation, Pseudomonas, Resorcinols, Spectrophotometry, Spectrophotometry, Ultraviolet}, issn = {0014-2956}, author = {Ohta, Y and Ribbons, D W} } @article {1707, title = {Citrate synthase.}, journal = {Curr Top Cell Regul}, volume = {10}, year = {1976}, month = {1976}, pages = {161-204}, keywords = {Adenosine Diphosphate, Adenosine Monophosphate, Adenosine Triphosphate, Amino Acids, Animals, Bacteria, Binding Sites, Cations, Divalent, Cations, Monovalent, Citrate (si)-Synthase, Dithionitrobenzoic Acid, Ketoglutaric Acids, Kinetics, Molecular Weight, NAD, NADP, Oxo-Acid-Lyases, Protein Binding, Species Specificity}, issn = {0070-2137}, author = {Weitzman, P D and Danson, M J} } @article {1738, title = {Bile acids. XLVII. 12alpha-Hydroxylation of precursors of allo bile acids by rabbit liver microsomes.}, journal = {Biochim Biophys Acta}, volume = {409}, year = {1975}, month = {1975 Nov 21}, pages = {249-57}, abstract = {

Rabbit liver microsomal preparations fortified with 0.1 mM NADPH effectively promote hydroxylation of [3beta-3H]- or [24-14C]allochenodeoxycholic acid or [5alpha,6alpha-3H2]5alpha-cholestane-3alpha,7alpha-diol to their respective 12alpha-hydroxyl derivatives in yields of about 25 or 65\% in 60 min. Minor amounts of other products are formed from the diol. The requirements for activity of rabbit liver microsomal 12alpha-hydroxylase resemble those of rat liver microsomes. Of a number of enzyme inhibitors studied only p-chloromercuribenzoate demonstrated a marked ability to inhibit the reaction with either tritiated substrate. There was no difference in the quantity of product produced from the tritiated acid or the 14C-labeled acid. No clear sex difference was found in activity of the enzyme, nor was an appreciable difference noted in activity of the enzyme between mature and immature animals.

}, keywords = {Aging, Animals, Bile Acids and Salts, Female, Kinetics, Male, Microsomes, Liver, Mixed Function Oxygenases, NADP, Oxidation-Reduction, Rabbits, Sex Factors}, issn = {0006-3002}, author = {Ali, S S and Elliott, W H} } @article {1710, title = {Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution.}, journal = {Biochem Biophys Res Commun}, volume = {66}, year = {1975}, month = {1975 Oct 27}, pages = {1173-9}, keywords = {Fourier Analysis, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Conformation, NAD, NADP, Structure-Activity Relationship, Temperature}, issn = {0006-291X}, author = {Bose, K S and Sarma, R H} } @article {1706, title = {Digitoxin metabolism by rat liver microsomes.}, journal = {Biochem Pharmacol}, volume = {24}, year = {1975}, month = {1975 Sep 1}, pages = {1639-41}, keywords = {Animals, Chromatography, Thin Layer, Digitoxigenin, Digitoxin, Hydroxylation, In Vitro Techniques, Male, Microsomes, Liver, NADP, Rats, Time Factors}, issn = {0006-2952}, author = {Schmoldt, A and Benthe, H F and Haberland, G} } @article {1727, title = {Inhibition of aldehyde reductase isoenzymes in human and rat brain.}, journal = {Biochem Pharmacol}, volume = {24}, year = {1975}, month = {1975 Oct 15}, pages = {1865-9}, keywords = {Aldehyde Oxidoreductases, Animals, Anticonvulsants, Barbiturates, Brain, Glutethimide, Humans, Hydantoins, In Vitro Techniques, Isoenzymes, Kinetics, NAD, NADP, Rats, Succinimides}, issn = {0006-2952}, author = {Ris, M M and Deitrich, R A and Von Wartburg, J P} }