Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts.

BACKGROUND: Efficient xylose fermentation still demands knowledge regarding xylose catabolism. In this study, metabolic flux analysis (MFA) and metabolomics were used to improve our understanding of xylose metabolism. Thus, a stoichiometric model was constructed to simulate the intracellular carbon flux and used to validate the metabolome data collected within xylose catabolic pathways of non-Saccharomyces xylose utilizing yeasts. RESULTS: A metabolic flux model was constructed using xylose fermentation data from yeasts Scheffersomyces stipitis, Spathaspora arborariae, and Spathaspora passalidarum. In total, 39 intracellular metabolic reactions rates were utilized validating the measurements of 11 intracellular metabolites, acquired by mass spectrometry. Among them, 80% of total metabolites were confirmed with a correlation above 90% when compared to the stoichiometric model. Among the intracellular metabolites, fructose-6-phosphate, glucose-6-phosphate, ribulose-5-phosphate, and malate are validated in the three studied yeasts. However, the metabolites phosphoenolpyruvate and pyruvate could not be confirmed in any yeast. Finally, the three yeasts had the metabolic fluxes from xylose to ethanol compared. Xylose catabolism occurs at twice-higher flux rates in S. stipitis than S. passalidarum and S. arborariae. Besides, S. passalidarum present 1.5 times high flux rate in the xylose reductase reaction NADH-dependent than other two yeasts. CONCLUSIONS: This study demonstrated a novel strategy for metabolome data validation and brought insights about naturally xylose-fermenting yeasts. S. stipitis and S. passalidarum showed respectively three and twice higher flux rates of XR with NADH cofactor, reducing the xylitol production when compared to S. arborariae. Besides then, the higher flux rates directed to pentose phosphate pathway (PPP) and glycolysis pathways resulted in better ethanol production in S. stipitis and S. passalidarum when compared to S. arborariae.

Molecularly Imprinted Polymer-Coated Probe Electrospray Ionization Mass Spectrometry Determines Phorbol Esters and Deoxyphorbol Metabolites in Jatropha curcas Leaves.

In this study, a molecularly imprinted polymer-coated probe electrospray ionization mass spectrometry (MIPCPESI-MS) method was developed for detection of phorbol esters (PEs) and deoxyphorbol metabolites in Jatropha curcas leaves. Such an approach was established by sticking on a metallic needle a molecularly imprinted polymer to particularly design a MIP-coated probe for selective sampling and ionization of PEs and deoxyphorbol metabolites. By a subsequent application of a high voltage and methanol, as spray solvent, ESI was generated for direct and rapid analysis under ambient and open-air conditions. MIP-coated probe exhibited a high sampling capacity of the PEs and its metabolites in methanolic extracts of J. curcas leaves compared with the non-imprinted polymer (NIP)-coated probe. MIPCPESI-MS allowed the detection of phorbol 12,13-diacetate (PDA) from J. curcas leaves with minimal sample preparation, and with detection limit and quantification reaching 0.28 µg/mL and 0.92 µg/mL, respectively. Also, good linearity was obtained with R2 > 0.99 and precision and accuracy values between 4.06-13.49% and - 1.60 to - 15.26%, respectively. The current method was successfully applied to screening methanolic extracts of six different J. curcas leaf genotypes (three toxic and three non-toxic). PDA and three PE deoxyphorbol metabolites were identified only from toxic genotypes, in which PDA was determined with concentration ranging from 222.19 ± 23.55 to 528.23 ± 19.72 µg/g. All these findings support that the MIPCPESI-MS method developed here has a high potential for the analysis of PEs in plant extracts enabling differentiation of toxic and non-toxic genotypes earlier in the leaves.

Uncovering the Formation of Color Gradients for Glucose Colorimetric Assays on Microfluidic Paper-Based Analytical Devices by Mass Spectrometry Imaging.

This study describes the use of mass spectrometry imaging with matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) to understand the color gradient generation commonly seen in microfluidic paper-based analytical devices (µPADs). The formation of color gradients significantly impacts assay sensitivity and reproducibility with µPADs but the mechanism for formation is poorly understood. The glucose enzymatic assay using potassium iodide (KI) as a chromogenic agent was selected to investigate the color gradient generated across a detection spot. Colorimetric measurements revealed that the relative standard deviation for the recorded pixel intensities ranged between 34 and 40%, compromising the analytical reliability. While a variety of hypotheses have been generated to explain this phenomenon, few studies have attempted to elucidate the mechanisms associated with its formation. Mass spectrometry imaging using MALDI and DESI was applied to understand the nonuniform color distribution on the detection zone. MALDI experiments were first explored to monitor the spatial distribution of the glucose oxidase and horseradish peroxidase mixture, before and after lateral flow assay with and without KI. MALDI(+)-TOF data revealed uniform enzyme distribution on the detection spots. On the other hand, after the complete assay DESI(-) measurements revealed a heterogeneous shape indicating the presence of iodide and triiodide ions at the zone edge. The reaction product (I3-) is transported by lateral flow toward the zone edge, generating the color gradient. Mass spectrometry imaging has been used for the first time to prove that color gradient forms as result of the mobility small molecules and not the enzyme distribution on µPAD surface.

Recombinant expression of Thermobifida fusca E7 LPMO in Pichia pastoris and Escherichia coli and their functional characterization.

The discovery of lytic polysaccharides monooxygenases copper dependent (LPMOs) revolutionized the classical concept that the cleavage of cellulose is a hydrolytic process in recent years. These enzymes carry out oxidative cleavage of cellulose (and other polysaccharides), acting synergistically with cellulases and other hydrolases. In fact, LPMOs have the potential for increasing the efficiency of the lignocellulosic biomass conversion in biofuels and high value chemicals. Among a small number of microbial LPMOs that have been characterized, some LPMOs were expressed and characterized biochemically from the bacteria Thermobifida fusca, using the host Escherichia coli. In this work, the E7 LPMO protein of T. fusca was expressed both in E. coli (native DNA sequence) and Pichia pastoris (codon-optimized DNA sequence), for further analysis of oxidative cleavage, with PASC (phosphoric acid swollen cellulose) and Avicel PH-101 substrates, using mass spectrometry analysis. Mass spectra results of Avicel PH-101 and PASC cleavages by purified E7 LPMO expressed in E. coli and in P. pastoris allowed the visualization of compounds corresponding to oxidized and non-oxidized oligosaccharides. Further optimization of reactions will be performed, since it was found only one degree of polymerization (DP 7). This work demonstrated that it is possible to produce the E7 LPMO from T. fusca in the host P. pastoris, and the recombinant protein was shown to be active on cellulose. The approach used in the present work could be an alternative to produce this bacterial LPMO for cellulose cleavage.

Water-soluble Tb3+ and Eu3+ complexes with ionophilic (ionically tagged) ligands as fluorescence imaging probes.

This article describes a straightforward and simple synthesis of ionically tagged water-soluble Eu(3+) and Tb(3+) complexes (with ionophilic ligands) applied for bioimaging of invasive mammal cancer cells (MDA-MB-231). Use of the task-specific ionic liquid 1-methyl-3-carboxymethyl-imidazolium chloride (MAI·Cl) as the ionophilic ligand (ionically tagged) proved to be a simple, elegant, and efficient strategy to obtain highly fluorescent water-soluble Eu(3+) (EuMAI) and Tb(3+) (TbMAI) complexes. TbMAI showed an intense bright green fluorescence emission selectively staining endoplasmic reticulum of MDA-MB-231 cells.

Synthesis of potentially bioactive PABA-related N-(aminoalkyl)lactamic amino acids and esters via selective S(N)Ar reactions.

Potentially bioactive N-(aminoalkyl)lactamic amino acids and esters were synthesized in satisfactory to good yields by S(N)Ar reactions of aromatic acids with N-(3-aminopropyl)lactams followed by esterification with tertiary amino alcohols. The addition-elimination S(N)Ar mechanism was confirmed by NMR and MS measurements.

Intrinsic acidity and electrophilicity of gaseous propargyl/allenyl carbocations.

The ion/molecule chemistry of four representative propagyl/allenyl cations 1-4 of the general formula R(1)CH(+)-C[triple bond]C-R (a) <--> R(1)CH=C=C(+)-R (b), that is, the reactive C(3)H(3)(+) ions of m/z 39 from EI of propargyl chloride (H(2)C(+)-C[triple bond]C-H, 1a), isomeric C(4)H(5)(+) ions of m/z 53 from EI of 3-butyne-2-ol (2a, H(2)C(+)-C[triple bond]C-CH(3)) and 2-butyne-1-ol (CH(3)-CH(+)-C[triple bond]C-H, 3a), and Ph-C(3)H(2)(+) ions of m/z 115 from 3-phenyl-2-propyn-1-ol (H(2)C(+)-C[triple bond]C-Ph, 4a) was studied via pentaquadrupole mass spectrometry. With pyridine, proton transfer was observed as the predominant process for 1 and the sole reaction channel for the isomeric 2 and 3, whereas 4 reacted preferentially by adduct formation. These outcomes were rationalized using DFT calculations from isodesmic proton transfer reactions. Similar reaction tendencies were observed with acetonitrile and acrylonitrile, with adduct formation appearing again as a minor pathway for 1, 2 and 4, and as a major reaction channel for 4. With 1,3-dioxolane, hydride abstraction was a dominant reaction, with proton transfer and adduct formation competing as side reactions. With 2,2-dimethyl-1,3-dioxolane, an interplay of reactions including methyl anion abstraction, proton transfer, hydride abstraction and adduct formation were observed depending on the ion structure, with 4 reacting again mainly by adduct formation. Proton transfer was also observed as a dominant process in reactions with ethanol for 1, 2 and 3, with 4 being nearly unreactive whereas no adduct formation was observed for any of the carbocations studied. Limited reactivity was exhibited by these ions in cycloaddition reaction with isoprene.

Fabric softeners: nearly instantaneous characterization and quality control of cationic surfactants by easy ambient sonic-spray ionization mass spectrometry.

A tiny droplet of typical samples of fabric softeners from different commercial brands placed on a smooth paper surface was subjected to easy ambient sonic-spray ionization mass spectrometry (EASI-MS). With no need for sample-preparation or pre-separation procedures, EASI-MS and EASI-MS/MS identify nearly instantaneously the main surfactants and the homologous series employed in their formulations. Adulterated and low quality samples containing no or less efficient softeners are also easily recognized.

Analysis of biodiesel and biodiesel-petrodiesel blends by high performance thin layer chromatography combined with easy ambient sonic-spray ionization mass spectrometry.

High performance thin layer chromatography (HPTLC) combined with on-spot detection and characterization via easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is applied to the analysis of biodiesel (B100) and biodiesel-petrodiesel blends (BX). HPTLC provides chromatographic resolution of major components whereas EASI-MS allows on-spot characterization performed directly on the HPTLC surface at ambient conditions. Constituents (M) are detected by EASI-MS in a one component-one ion fashion as either [M + Na](+) or [M + H](+). For both B100 and BX samples, typical profiles of fatty acid methyl esters (FAME) detected as [FAME + Na](+) ions allow biodiesel typification. The spectrum of the petrodiesel spot displays a homologous series of protonated alkyl pyridines which are characteristic for petrofuels (natural markers). The spectrum for residual or admixture oil spots is characterized by sodiated triglycerides [TAG + Na](+). The application of HPTLC to analyze B100 and BX samples and its combination with EASI-MS for on-spot characterization and quality control is demonstrated.

Single-shot biodiesel analysis: nearly instantaneous typification and quality control solely by ambient mass spectrometry.

Using a simple and easily implemented desorption/ionization mass spectrometry technique, a tiny droplet of biodiesel placed on the surface of a sheet of paper is analyzed directly and nearly instantaneously under ambient conditions. No pre-separation or sample preparation is required, and clean mass spectra are obtained with great simplicity. In the positive ion mode, easy ambient sonic-spray ionization mass spectrometry, EASI(+)-MS, provides typical profiles of the major components of biodiesel samples, that is, either methyl esters (FAME) or ethyl esters (FAEE) of the natural fatty acids and triglycerides (TAG) from residual oil or oil from adulteration. Each FAME (FAEE) or TAG molecule is detected as a single sodiated molecule, [M + Na] (+) with relative intensities that correlate well with the known fatty acid profiles of the oil. Using EASI(-)-MS, typical and complementary profiles of free fatty acids (FFA) are obtained, which are detected in their deprotonated forms [FAA - H] (-). A general, single-shot approach for biodiesel analysis is therefore described, and samples from different feedstocks, from blends with petrodiesel, or from either methanol or ethanol trans-esterification are readily typified and major parameters of quality accessed.