SAR11 Cells Rely on Enzyme Multifunctionality To Metabolize a Range of Polyamine Compounds.

In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations at seawater pH produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells uptake and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, "Candidatus Pelagibacter" strain HTCC7211 and "Candidatus Pelagibacter ubique" strain HTCC1062. Both strains took up all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but polyamines did not fully substitute for their requirements of glycine (or related compounds) or pyruvate (or related compounds). Our data suggest that potABCD transports all five polyamines and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they metabolize. IMPORTANCE Genome streamlining in SAR11 bacterioplankton has resulted in a small repertoire of genes, yet paradoxically, they consume a substantial fraction of primary production in the oceans. Enzyme multifunctionality, referring to enzymes that are adapted to have broader substrate and catalytic range than canonically defined, is hypothesized to be an adaptation that increases the range of organic compounds metabolized by cells in environments where selection favors genome minimization. We provide experimental support for this hypothesis by demonstrating that SAR11 cells take up and metabolize multiple polyamine compounds and propose that a small set of multifunctional enzymes catalyze this metabolism. We report that polyamine uptake rates can exceed metabolic rates, resulting in both high intracellular concentrations of these nitrogen-rich compounds (in comparison to native polyamine levels) and an increase in cell size.

Amelioration of Metabolic Syndrome-Associated Cognitive Impairments in Mice via a Reduction in Dietary Fat Content or Infusion of Non-Diabetic Plasma.

Obesity, metabolic syndrome (MetS) and type 2 diabetes (T2D) are associated with decreased cognitive function. While weight loss and T2D remission result in improvements in metabolism and vascular function, it is less clear if these benefits extend to cognitive performance. Here, we highlight the malleable nature of MetS-associated cognitive dysfunction using a mouse model of high fat diet (HFD)-induced MetS. While learning and memory was generally unaffected in mice with type 1 diabetes (T1D), multiple cognitive impairments were associated with MetS, including deficits in novel object recognition, cued fear memory, and spatial learning and memory. However, a brief reduction in dietary fat content in chronic HFD-fed mice led to a complete rescue of cognitive function. Cerebral blood volume (CBV), a measure of vascular perfusion, was decreased during MetS, was associated with long term memory, and recovered following the intervention. Finally, repeated infusion of plasma collected from age-matched, low fat diet-fed mice improved memory in HFD mice, and was associated with a distinct metabolic profile. Thus, the cognitive dysfunction accompanying MetS appears to be amenable to treatment, related to cerebrovascular function, and mitigated by systemic factors.

Analysis of dibenzo[def,p]chrysene-deoxyadenosine adducts in wild-type and cytochrome P450 1b1 knockout mice using stable-isotope dilution UHPLC-MS/MS.

The polycyclic aromatic hydrocarbon (PAH), dibenzo[def,p]chrysene (DBC; also known as dibenzo[a,l]pyrene), is a potent carcinogen in animal models and a class 2A human carcinogen. Recent investigations into DBC-mediated toxicity identified DBC as a potent immunosuppressive agent similar to the well-studied immunotoxicant 7,12-dimethylbenz[a]anthracene (DMBA). DBC, like DMBA, is bioactivated by cytochrome P450 (CYP) 1B1 and forms the reactive metabolite DBC-11,12-diol-13,14-epoxide (DBCDE). DBCDE is largely responsible for the genotoxicity associated with DBC exposure. The immunosuppressive properties of several PAHs are also linked to genotoxic mechanisms. Therefore, this study was designed to identify DBCDE-DNA adduct formation in the spleen and thymus of wild-type and cytochrome P450 1b1 (Cyp1b1) knockout (KO) mice using a highly sensitive stable-isotope dilution UHPLC-MS/MS method. Stable-isotope dilution UHPLC-MS/MS identified the major DBC adducts (±)-anti-cis-DBCDE-dA and (±)-anti-trans-DBCDE-dA in the lung, liver, and spleen of both WT and Cyp1b1 KO mice. However, adduct formation in the thymus was below the level of quantitation for our method. Additionally, adduct formation in Cyp1b1 KO mice was significantly reduced compared to wild-type (WT) mice receiving DBC via oral gavage. In conclusion, the current study identifies for the first time DBCDE-dA adducts in the spleen of mice supporting the link between genotoxicity and immunosuppression, in addition to supporting previous studies identifying Cyp1b1 as the primary CYP involved in DBC bioactivation to DBCDE. The high levels of DBC-DNA adducts identified in the spleen, along with the known high levels of Cyp1b1 expression in this organ, supports further investigation into DBC-mediated immunotoxicity.

Discovery of a SAR11 growth requirement for thiamin's pyrimidine precursor and its distribution in the Sargasso Sea.

Vitamin traffic, the production of organic growth factors by some microbial community members and their use by other taxa, is being scrutinized as a potential explanation for the variation and highly connected behavior observed in ocean plankton by community network analysis. Thiamin (vitamin B1), a cofactor in many essential biochemical reactions that modify carbon-carbon bonds of organic compounds, is distributed in complex patterns at subpicomolar concentrations in the marine surface layer (0-300 m). Sequenced genomes from organisms belonging to the abundant and ubiquitous SAR11 clade of marine chemoheterotrophic bacteria contain genes coding for a complete thiamin biosynthetic pathway, except for thiC, encoding the 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) synthase, which is required for de novo synthesis of thiamin's pyrimidine moiety. Here we demonstrate that the SAR11 isolate 'Candidatus Pelagibacter ubique', strain HTCC1062, is auxotrophic for the thiamin precursor HMP, and cannot use exogenous thiamin for growth. In culture, strain HTCC1062 required 0.7 zeptomoles per cell (ca. 400 HMP molecules per cell). Measurements of dissolved HMP in the Sargasso Sea surface layer showed that HMP ranged from undetectable (detection limit: 2.4 pM) to 35.7 pM, with maximum concentrations coincident with the deep chlorophyll maximum. In culture, some marine cyanobacteria, microalgae and bacteria exuded HMP, and in the Western Sargasso Sea, HMP profiles changed between the morning and evening, suggesting a dynamic biological flux from producers to consumers.

Pyrolysis of cellulose under ammonia leads to nitrogen-doped nanoporous carbon generated through methane formation.

Here, we present a simple one-step fabrication methodology for nitrogen-doped (N-doped) nanoporous carbon membranes via annealing cellulose filter paper under NH3. We found that nitrogen doping (up to 10.3 at %) occurs during cellulose pyrolysis under NH3 at as low as 550 °C. At 700 °C or above, N-doped carbon further reacts with NH3, resulting in a large surface area (up to 1973.3 m(2)/g). We discovered that the doped nitrogen, in fact, plays an important role in the reaction, leading to carbon gasification. CH4 was experimentally detected by mass spectrometry as a product in the reaction between N-doped carbon and NH3. When compared to conventional activated carbon (1533.6 m(2)/g), the N-doped nanoporous carbon (1326.5 m(2)/g) exhibits more than double the unit area capacitance (90 vs 41 mF/m(2)).

Caffeoylquinic acids in Centella asiatica protect against amyloid-ß toxicity.

The accumulation of amyloid-ß (Aß) is a hallmark of Alzheimer's disease and is known to result in neurotoxicity both in vivo and in vitro. We previously demonstrated that treatment with the water extract of Centella asiatica (CAW) improves learning and memory deficits in Tg2576 mice, an animal model of Aß accumulation. However the active compounds in CAW remain unknown. Here we used two in vitro models of Aß toxicity to confirm this neuroprotective effect and identify several active constituents of the CAW extract. CAW reduced Aß-induced cell death and attenuated Aß-induced changes in tau expression and phosphorylation in both the MC65 and SH-SY5Y neuroblastoma cell lines. We confirmed and quantified the presence of several mono- and dicaffeoylquinic acids (CQAs) in CAW using chromatographic separation coupled to mass spectrometry and ultraviolet spectroscopy. Multiple dicaffeoylquinic acids showed efficacy in protecting MC65 cells against Aß-induced cytotoxicity. Isochlorogenic acid A and 1,5-dicaffeoylquinic acid were found to be the most abundant CQAs in CAW, and the most active in protecting MC65 cells from Aß-induced cell death. Both compounds showed neuroprotective activity in MC65 and SH-SY5Y cells at concentrations comparable to their levels in CAW. Each compound not only mitigated Aß-induced cell death, but was able to attenuate Aß-induced alterations in tau expression and phosphorylation in both cell lines, as seen with CAW. These data suggest that CQAs are active neuroprotective components in CAW, and therefore are important markers for future studies on CAW standardization, bioavailability, and dosing.

Electrospray Quadrupole Travelling Wave Ion Mobility Time-of-Flight Mass Spectrometry for the Detection of Plasma Metabolome Changes Caused by Xanthohumol in Obese Zucker (fa/fa) Rats.

This study reports on the use of traveling wave ion mobility quadrupole time-of-flight (ToF) mass spectrometry for plasma metabolomics. Plasma metabolite profiles of obese Zucker fa/fa rats were obtained after the administration of different oral doses of Xanthohumol; a hop-derived dietary supplement. Liquid chromatography coupled data independent tandem mass spectrometry (LC-MSE) and LC-ion mobility spectrometry (IMS)-MSE acquisitions were conducted in both positive and negative modes using a Synapt G2 High Definition Mass Spectrometry (HDMS) instrument. This method provides identification of metabolite classes in rat plasma using parallel alternating low energy and high energy collision spectral acquisition modes. Data sets were analyzed using pattern recognition methods. Statistically significant (p < 0.05 and fold change (FC) threshold > 1.5) features were selected to identify the up-/down-regulated metabolite classes. Ion mobility data visualized using drift scope software provided a graphical read-out of differences in metabolite classes.

Diapocynin and apocynin administration fails to significantly extend survival in G93A SOD1 ALS mice.

NADPH oxidase has recently been identified as a promising new therapeutic target in ALS. Genetic deletion of NADPH oxidase (Nox2) in the transgenic SOD1(G93A) mutant mouse model of ALS was reported to increase survival remarkably by 97 days. Furthermore, apocynin, a widely used inhibitor of NADPH oxidase, was observed to dramatically extend the survival of the SOD1(G93A) ALS mice even longer to 113 days (Harraz et al. J Clin Invest 118: 474, 2008). Diapocynin, the covalent dimer of apocynin, has been reported to be a more potent inhibitor of NADPH oxidase. We compared the protection of diapocynin to apocynin in primary cultures of SOD1(G93A)-expressing motor neurons against nitric oxide-mediated death. Diapocynin, 10 µM, provided significantly greater protection compared to apocynin, 200 µM, at the lowest statistically significant concentrations. However, administration of diapocynin starting at 21 days of age in the SOD1(G93A)-ALS mouse model did not extend lifespan. Repeated parallel experiments with apocynin failed to yield protection greater than a 5-day life extension in multiple trials conducted at two separate institutions. The maximum protection observed was an 8-day extension in survival when diapocynin was administered at 100 days of age at disease onset. HPLC with selective ion monitoring by mass spectrometry revealed that both apocynin and diapocynin accumulated in the brain and spinal cord tissue to low micromolar concentrations. Diapocynin was also detected in the CNS of apocynin-treated mice. The failure to achieve significant protection with either apocynin or diapocynin raises questions about the utility for treating ALS patients.

High resolution mass analysis of N- and C-terminal negative ions resulting from resonance electron capture by aliphatic amino acids.

High mass resolving power was applied to study resonance electron capture by glycine, alanine, and valine, and accurate mass measurements helped to distinguish between some negative ions having the same nominal masses. It was established that the C- and N-terminal negative ions of the same nominal masses were formed at different electron energies from different resonance states. The typical fragmentation pathways in deprotonated amino acids via loss of water initiated by collisional activation were not observed upon resonant electron capture by aliphatic amino acids. Instead, [M-18](-) negative ions in the vicinity of 5 eV were found to be associated with simultaneous loss of either ammonia and a hydrogen atom or an amino group and a hydrogen molecule.

Fragmentation of peptide negative molecular ions induced by resonance electron capture.

A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1-2 eV) energy REC are of the same types as those observed in electron capture/transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of z(n)-1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M-H](-) NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of c(n)+1 ions. Instead, c(n) ions arose without hydrogen/proton transfer albeit with lower abundances than that observed for z(n)-1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the c(n) ions than for the z(n)-1 ions. The mechanisms for the N-C(alpha) bond cleavage are discussed.

Charge-remote metastable ion decomposition of free fatty acids under FAB MS: evidence for biradical ion structures.

Classical charge-remote fragmentation (CRF) of a series of long-chain saturated and monounsaturated fatty acid anions, a well-known phenomenon under collisional activation conditions, is observed for the first time during fast atom bombardment of the analyte-matrix mixture without collisional activation. The process is efficient enough to allow collision-induced dissociation and metastable ion decomposition MS/MS spectra of any charge-remote [M-H2-(CH2)n]- fragments as well as spectra of neutral losses to be recorded. The results obtained are in contradiction to the generally accepted theory that CRF results exclusively in terminally unsaturated carboxylate anions. The new results indicate that a multistep radical mechanism is involved in CRF ion formation. The first step of the process appears to be accompanied by hydrogen elimination that occurs randomly throughout the molecule. The primary fragment radical ions formed can decompose further with the formation of the next generation of CRF ions.

Quantitative determination of uracil residues in Escherichia coli DNA: Contribution of ung, dug, and dut genes to uracil avoidance.

The steady-state levels of uracil residues in DNA extracted from strains of Escherichia coli were measured and the influence of defects in the genes for uracil-DNA glycosylase (ung), double-strand uracil-DNA glycosylase (dug), and dUTP pyrophosphatase (dut) on uracil accumulation was determined. A sensitive method, called the Ung-ARP assay, was developed that utilized E. coli Ung, T4pdg, and the Aldehyde Reactive Probe reagent to label abasic sites resulting from uracil excision with biotin. The limit of detection was one uracil residue per million DNA nucleotides (U/10(6)nt). Uracil levels in the genomic DNA of E. coli JM105 (ung+ dug+) were at the limit of detection, as were those of an isogenic dug mutant, regardless of growth phase. Inactivation of ung in JM105 resulted in 31+/-2.6 U/10(6)nt during early log growth and 19+/-1.7 U/10(6)nt in saturated phase. An ung dug double mutant (CY11) accumulated 33+/-2.9 U/10(6)nt and 23+/-1.8U/10(6)nt during early log and saturated phase growth, respectively. When cultures of CY11 were supplemented with 20 ng/ml of 5-fluoro-2'-deoxyuridine, uracil levels in early log phase growth DNA rose to 125+/-1.7 U/10(6)nt. Deoxyuridine supplementation reduced the amount of uracil in CY11 DNA, but uridine did not. Levels of uracil in DNA extracted from CJ236 (dut-1 ung-1) were determined to be 3000-8000 U/10(6)nt as measured by the Ung-ARP assay, two-dimensional thin-layer chromatography of metabolically-labeled 32P DNA, and LC/MS of uracil and thymine deoxynucleosides. DNA sequencing revealed that the sole molecular defect in the CJ236 dUTP pyrophosphatase gene was a C-->T transition mutation that resulted in a Thr24Ile amino acid change.

A resonant electron capture time-of-flight MS with trochoidal electron monochromator.

A prototype electron monochromator (EM) reflectron time-of-flight (TOF) mass spectrometer has been constructed and demonstrated to record resonant electron capture (REC) mass spectra of electron-capturing compounds. The electron energy is ramped from -1.7 to +25 eV at a preset frequency, and the energy spread of the electron beam at 15 nA is 100 meV or better. Ions are orthogonally extracted into the analyzer at a frequency of up to 80 kHz while maintaining an upper m/z-limit of at least 300 and a mass resolving power of approximately 1000. A complete REC mass spectrum, which includes an effective yield versus electron energy curve for each negative ion formed from the compound being analyzed, typically takes several days to produce with a quadrupole or magnetic sector mass spectrometer. With the EM TOF described in this work, three-dimensional negative ion electron capture spectra are recorded in an interval on the order of only 1 s and displayed in real time. This new analytical capability could make it possible to perform GC REC mass spectrometry as well as easier (a) to measure the temperature dependence of REC cross sections, (b) to determine enthalpies of negative ion formation (accurate determination of the enthalpy of ion formation requires knowledge of the translational energy released during a dissociative capture event), and (c) to provide complete thermochemical descriptions of dissociative electron attachment by measuring ion lifetimes.