Real-time Nuclear Magnetic Resonance Research Articles

Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy.

Primases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein-DNA complex remains active in the solid-state NMR rotor and that time-resolved 31P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.

Ligand-Based Competition Binding by Real-Time 19F NMR in Human Cells.

The development of more effective drugs requires knowledge of their bioavailability and binding efficacy directly in the native cellular environment. In-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating ligand-target interactions directly in living cells. However, the target molecule may be NMR-invisible due to interactions with cellular components, while observing the ligand by 1H NMR is impractical due to the cellular background. Such limitations can be overcome by observing fluorinated ligands by 19F in-cell NMR as they bind to the intracellular target. Here we report a novel approach based on real-time in-cell 19F NMR that allows measuring ligand binding affinities in human cells by competition binding, using a fluorinated compound as a reference. The binding of a set of compounds toward Hsp90α was investigated. In principle, this approach could be applied to other pharmacologically relevant targets, thus aiding the design of more effective compounds in the early stages of drug development.

Pore-pressure and stress-coupled creep behavior in deep coal: Insights from real-time NMR analysis

Understanding the variations in microscopic pore-fracture structures (MPFS) during coal creep under pore pressure and stress coupling is crucial for coal mining and effective gas treatment. In this manuscript, a triaxial creep test on deep coal at various pore pressures using a test system that combines in-situ mechanical loading with real-time nuclear magnetic resonance (NMR) detection was conducted. Full-scale quantitative characterization, online real-time detection, and visualization of MPFS during coal creep influenced by pore pressure and stress coupling were performed using NMR and NMR imaging (NMRI) techniques. The results revealed that seepage pores and microfractures (SPM) undergo the most significant changes during coal creep, with creep failure gradually expanding from dense primary pore fractures. Pore pressure presence promotes MPFS development primarily by inhibiting SPM compression and encouraging adsorption pores (AP) to evolve into SPM. Coal enters the accelerated creep stage earlier at lower stress levels, resulting in more pronounced creep deformation. The connection between the micro and macro values was established, demonstrating that increased porosity at different pore pressures leads to a negative exponential decay of the viscosity coefficient. The Newton dashpot in the ideal viscoplastic body and the Burgers model was improved using NMR experimental results, and a creep model that considers pore pressure and stress coupling using variable-order fractional operators was developed. The model’s reasonableness was confirmed using creep experimental data. The damage-state adjustment factors ω and β were identified through a parameter sensitivity analysis to characterize the effect of pore pressure and stress coupling on the creep damage characteristics (size and degree of difficulty) of coal.

Intracellular pyruvate-lactate-alanine cycling detected using real-time nuclear magnetic resonance spectroscopy of live cells and isolated mitochondria.

Pyruvate, an end product of glycolysis, is a master fuel for cellular energy. A portion of cytosolic pyruvate is transported into mitochondria, while the remaining portion is converted reversibly into lactate and alanine. It is suggested that cytosolic lactate and alanine are transported and metabolized inside mitochondria. However, such a mechanism continues to be a topic of intense debate and investigation. As a part of gaining insight into the metabolic fate of the cytosolic lactate and alanine; in this study, the metabolism of mouse skeletal myoblast cells (C2C12) and their isolated mitochondria was probed utilizing stable isotope-labeled forms of the three glycolysis products, viz. [3-13 C1 ]pyruvate, [3-13 C1 ]lactate, and [3-13 C1 ]alanine, as substrates. The uptake and metabolism of each substrate was monitored, separately, in real-time using 1 H-13 C 2D nuclear magnetic resonance (NMR) spectroscopy. The dynamic variation of the levels of the substrates and their metabolic products were quantitated as a function of time. The results demonstrate that all three substrates were transported into mitochondria, and each substrate was metabolized to form the other two metabolites, reversibly. These results provide direct evidence for intracellular pyruvate-lactate-alanine cycling, in which lactate and alanine produced by the cytosolic pyruvate are transported into mitochondria and converted back to pyruvate. Such a mechanism suggests a role for lactate and alanine to replenish mitochondrial pyruvate, the primary source for adenosine triphosphate (ATP) synthesis through oxidative phosphorylation and the electron transport chain. The results highlight the potential of real-time NMR spectroscopy for gaining new insights into cellular and subcellular functions.

Planar Waveguide NMR Gradients (B0 and B1) for spatiotemporal Investigations of Anticancer Drug Concentration in 3D Cancer Cell Cultures

Despite the progression in cancer therapeutic approaches, cancer is still the leading cause of death worldwide with a steadily increasing incidence rate. In Jordan, CRC is the most common type of cancer among men and the second most common among women, while being one of the most accruing cancers in Germany.
 The difficulties in cancer treatments arise from the poor correlation between in vivo and in in vitro anti-cancer drug testing results and cancer cells resistance to chemotherapy, which are attributed to the heterogeneity of cancer cells, and the interaction of cancer cells with non-cancerous cells in the tumor microenvironment (TME). In addition to, the several mechanisms, that governs DNA damages repair, epigenetics, epithelial to mesenchymal transition (EMT).
 Cell culture techniques have been developed to construct in vitro multicellular cancer spheroids (MTCS) that mimic cell-cells interaction and the cellular organization in the TME. They also illustrate the proliferation gradient of solid tumors, and the nutrition and gas supply to cancer cells at different depth in the spheroid. Therefore, they are considered an excellent in vitro cancer model to study the efficiency and to investigate the penetration depth of the anti-cancer materials.
 Nuclear Magnetic Resonance (NMR) spectroscopy is a reliable analytical method that gives comprehensive and rich chemical information, along with high speciation performance. It is one of the major noninvasive tools for metabolomics, therefore it has been utilized to study the metabolic profiling of freshly isolated- non-destructed tissues, and living in vitro cellular models.
 A micro-imaging technique for real-time NMR investigations is developed to study the penetration depth, rate, and effective diffusion coefficients of anti-cancer materials through cancer spheroids. This technique is based on our patented invention of planar waveguide micro slot NMR detector with on board thermal regulator integrated and a microfluidic device. Based on this innovative development, we are able to perform real-time magnetic resonance spectroscopic imaging (MRSI) on a living synthetic tissue constructed in micrometer scale to monitor drug penetration and diffusion, while providing spectroscopic information about the production and degradation of metabolites in picomoles concentrations.

Real-time NMR analysis of polyhydroxyalkanoate synthase reaction that synthesizes block copolymer comprising glycolate and 3-hydroxybutyrate

The sequence-regulating polyhydroxyalkanoate (PHA) synthase PhaCAR spontaneously synthesizes the homo-random block copolymer, poly[3-hydroxybutyrate (3HB)]-b-poly[glycolate (GL)-ran-3HB]. In this study, a real-time in vitro chasing system was established using a high-resolution 800 MHz nuclear magnetic resonance (NMR) and 13C-labeled monomers to monitor the polymerization of GL-CoA and 3HB-CoA into this atypical copolymer. Consequently, PhaCAR initially consumed only 3HB-CoA and subsequently consumed both substrates. The structure of the nascent polymer was analyzed by extracting it with deuterated hexafluoro-isopropanol. In the primary reaction product, a 3HB-3HB dyad was detected, and GL-3HB linkages were subsequently formed. According to these results, the P(3HB) homopolymer segment is synthesized prior to the random copolymer segment. This is the first report of its kind which proposes the application of real-time NMR to a PHA synthase assay, paving the way for elucidating the mechanisms of PHA block copolymerization.

Flow NMR system development for real-time in situ multiple detection of direct methanol fuel cell exhausts

Understanding the electrochemical reaction mechanisms of energy conversion and storage systems is essential for improving their performance. Nuclear magnetic resonance (NMR) spectroscopy is an excellent quantitative and qualitative analysis method for investigating electrochemical reactions. We developed in situ real-time 2H flow NMR spectroscopy using a toroid cavity detector to simultaneously acquire the spectra of the anode and cathode exhausts of a direct methanol fuel cell. We used deuterium-enriched methanol (CD3OH) as fuel in order to obtain background-free spectra. Besides HOD, the CD3OH crossed over from the anode was observed in the cathode exhaust. The amount of CO2 gas, which is impossible to detect with ex situ NMR spectroscopy, was proportional to the HOD amount and current generated during the cell operation at a given potential. Therefore, in situ real-time analysis enabled us to identify and quantify the anode and cathode exhaust chemical components, including the gaseous products, such as CO2, of a fuel cell. This explains differences in the fuel cell performance by identifying generated and consumed chemicals and their pathways in the cells at respective conditions. Hence, our results demonstrate that this in situ real-time flow NMR method is applicable to studying the reaction mechanism of various other liquid-flowing chemical reaction systems besides fuel cells. Furthermore, it may open a new door for designing advanced materials.

Experimental evaluation of the dynamic water-blocking effect in coalbed methane reservoir

Field observations indicate that almost 59% of coalbed methane (CBM) wells in the southern Qinshui Basin showed insufficient daily gas production (∼600 m3/t); this is caused by the water-blocking effect (WBE) attributed to the invasion of fracturing fluids or the accumulation of formation water. WBE can cause serious damages to the low-permeability reservoir but has not been paid sufficient attention to in CBM studies. To enhance understanding of the dynamic WBE in the multiphase flow process, we conducted core flooding experiments on two typical Chinese bituminous coal and anthracite coal samples. During the flooding experiments, real-time nuclear magnetic resonance (NMR) measurements of the change of water signal in the core were used to calculate the gas-water relative permeability and to evaluate the dynamic WBE. The results highlight that a more pronounced WBE occurred in anthracite coal compared with bituminous coal. The gas breakthrough model can calculate the gas breakthrough time, which is a useful parameter for evaluating water blocking. The water-blocking threshold pressure gradient (TPG) was determined based on experimental data. The results reveal that the water-blocking TPGs for both samples follow a positive power-law relationship with the normalized water saturation. The water-blocking TPG is approximately an order of magnitude higher than that of the conventional gas TPG. A high water-blocking TPG value reflects stronger gas/water interference during multiphase flow, exerting a negligible impact on the gas migration through the coalbed, which should be prioritized in CBM production. The implications of this study are important for a better understanding of the interaction mechanism of gas and water transport in coal reservoirs during the gas production process.

Learnings From a New Slimhole LWD NMR Technology

This paper presents recent results obtained from a new 4.75-in. logging-while-drilling (LWD) nuclear magnetic resonance (NMR) tool. Data from several wells provided real-time operational insight and new petrophysical learnings. The new LWD technology offers an innovative capability to simultaneously measure NMR T1 and T2 distributions with reduced sensitivity to drilling mud conductivity and a real-time sensor motion-warning system. The real-time T1 and T2 spectra compare favorably with the data set retrieved from the tool memory. The LWD NMR measurements were followed by wireline (WL) NMR logging for comparison in three wells. In carbonate reservoirs, the main objective was to evaluate the new NMR tool’s capability in resolving carbonate pore size with slow NMR relaxation rates. Another set of NMR logs contained time-lapse repeat passes in a well drilled with oil-based mud (OBM) that traversed a clastic reservoir. The sequence of measurements identified rock types and provided a unique insight into the mud filtrate invasion process. In a carbonate reservoir, the LWD NMR real-time partial porosity estimates were in excellent agreement with the core-calibrated WL micro-, meso-, and macropore volumes. Another carbonate formation contained high-permeability layers embedded in a microporous rock, where the real-time LWD NMR logs successfully located the high-quality rock zones, later verified by WL logging. In the clastic reservoir, the while-drilling LWD NMR data indicated native light hydrocarbons, whereas the subsequent LWD reaming and WL NMR passes showed a displacement of native hydrocarbons by oil-based mud filtrate (OBMF). The native hydrocarbon signature observed by the LWD NMR tool was in good agreement with the mud gas log. OBMF invasion occurred shortly after drilling, indicated by the differences observed in the LWD NMR relogged data acquired several hours after the while-drilling pass. The WL NMR data, logged about 4 days after drilling, showed advanced stages of OBMF invasion, including formation water displacement and wettability changes in intermediate and large pores. Finally, the environmental noise remained low in the LWD NMR data set acquired in a well in which the mud salinity changed by several folds, indicating that mud salinity had little effect on the quality of LWD NMR logs in slim holes. The new slimhole LWD NMR technology demonstrated its robust capability to provide T1 and T2 logs through several examples. For the first time, a time-lapse comparison of NMR logs showed that OBMF invasion could occur in silty sands with high capillary-bound fluid fractions.

Design of Low Cost Real-time Nuclear Magnetic Resonance

Design of Low Cost Real-time Nuclear Magnetic Resonance

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics.

The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i)signal-to-noise due to the time limitations and (ii)synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

Flexibility of Oxidized and Reduced States of the Chloroplast Regulatory Protein CP12 in Isolation and in Cell Extracts.

In the chloroplast, Calvin–Benson–Bassham enzymes are active in the reducing environment created in the light by electrons from the photosystems. In the dark, these enzymes are inhibited, mainly caused by oxidation of key regulatory cysteine residues. CP12 is a small protein that plays a role in this regulation with four cysteine residues that undergo a redox transition. Using amide-proton exchange with solvent, measured by nuclear magnetic resonance (NMR) and mass-spectrometry, we confirmed that reduced CP12 is intrinsically disordered. Using real-time NMR, we showed that the oxidation of the two disulfide bridges is simultaneous. In oxidized CP12, the C23–C31 pair is in a region that undergoes a conformational exchange in the NMR-intermediate timescale. The C66–C75 pair is in the C-terminus that folds into a stable helical turn. We confirmed that these structural states exist in a physiologically relevant environment: a cell extract from Chlamydomonas reinhardtii. Consistent with these structural equilibria, the reduction is slower for the C66–C75 pair than for the C23–C31 pair. The redox mid-potentials for the two cysteine pairs differ and are similar to those found for glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase, consistent with the regulatory role of CP12.

Thermodynamic Stability and Aggregation Kinetics of EF Helix and EF Loop Variants of Transthyretin.

Misfolding and aggregation of transthyretin (TTR) are linked to amyloid disease. Amyloidosis occurs when the TTR homotetramer dissociates into aggregation-prone monomers that self-assemble into amyloid. In familial transthyretin amyloidosis, hereditary amino acid substitutions destabilize TTR and promote aggregation. In this work, we used 19F nuclear magnetic resonance (NMR) to determine the effect of mutations in the EF helix (Y78F, K80D, K80E, and A81T) and EF loop (G83R and I84S) on the aggregation kinetics and stability of the TTR tetramer and monomer. The EF region acts as a scaffold that stabilizes interactions in both the strong and weak dimer interfaces of the tetramer and is the site of a cluster of pathogenic mutations. K80D and K80E are non-natural mutants that destabilize the EF helix and yield an equilibrium mixture of tetramer and monomer at neutral pH, providing a unique opportunity to determine the thermodynamic parameters for tetramer assembly under nondenaturing conditions. Of the pathogenic mutants studied, only A81T formed appreciable monomer at neutral pH. Real-time 19F NMR measurements showed that the pathogenic Y78F mutation accelerates aggregation by destabilizing both the tetrameric and monomeric species. The pathogenic mutations A81T, G83R, and I84S destabilize the monomer and increase its aggregation rate by disrupting a Schellman helix C-capping motif. These studies provide new insights into the mechanism by which relatively subtle mutations that affect tetramer or monomer stability promote entry of TTR into the dissociation-aggregation pathway.

Real-Time In-Cell NMR Reveals the Intracellular Modulation of GTP-Bound Levels of RAS

The small guanosine triphosphatase (GTPase) RAS serves as a molecular switch in signal transduction, and its mutation and aberrant activation are implicated in tumorigenesis. Here, we perform real-time, in-cell nuclear magnetic resonance (NMR) analyses of non-farnesylated RAS to measure time courses of the fraction of the active GTP-bound form (fGTP) within cytosol of live mammalian cells. The observed intracellular fGTP is significantly lower than that measured invitro for wild-type RAS as well as oncogenic mutants, due to both decrease of the guanosine diphosphate (GDP)-GTP exchange rate (kex) and increase of GTP hydrolysis rate (khy). Invitro reconstitution experiments show that highly viscous environments promote a reduction of kex, whereas the increase of khy is stimulated by unidentified cytosolic proteins. This study demonstrates the power of in-cell NMR to directly detect the GTP-bound levels of RAS in mammalian cells, thereby revealing that the khy and kex of RAS are modulated by various intracellular factors.

Assessing the Onset of Calcium Phosphate Nucleation by Hyperpolarized Real-Time NMR.

We report an experimental approach for high-resolution real-time monitoring of transiently formed species occurring during the onset of precipitation of ionic solids from solution. This is made possible by real-time nuclear magnetic resonance (NMR) monitoring using dissolution dynamic nuclear polarization (D-DNP) to amplify signals of functional intermediates and is supported by turbidimetry, cryogenic electron microscopy, and solid-state NMR measurements. D-DNP can provide drastic signal improvements in NMR signal amplitudes, permitting dramatic reductions in acquisition times and thereby enabling us to probe fast interaction kinetics such as those underlying formation of prenucleation species (PNS) that precede solid–liquid phase separation. This experimental strategy allows for investigation of the formation of calcium phosphate (CaP)-based minerals by 31P NMR—a process of substantial industrial, geological, and biological interest. Thus far, many aspects of the mechanisms of CaP nucleation remain unclear due to the absence of experimental methods capable of accessing such processes on sufficiently short time scales. The approach reported here aims to address this by an improved characterization of the initial steps of CaP precipitation, permitting detection of PNS by NMR and determination of their formation rates, exchange dynamics, and sizes. Using D-DNP monitoring, we find that under our conditions (i) in the first 2 s after preparation of oversaturated calcium phosphate solutions, PNS with a hydrodynamic radius of Rh ≈ 1 nm is formed and (ii) following this rapid initial formation, the entire crystallization processes proceed on considerably longer time scales, requiring >20 s to form the final crystal phase.

Real-time benchtop NMR spectroscopy for the online monitoring of sucrose hydrolysis

The online monitoring of chemical reactions by using benchtop Nuclear Magnetic Resonance (NMR) spectroscopy has become increasingly attractive for the past few years. The use of quantitative online NMR spectroscopy is a promising alternative to traditional analytical methods with its rapid, quantitative and non-invasive nature that makes it applicable to complex and diverse biochemical mixtures like food systems. In this study, sucrose hydrolysis by invertase was chosen as a model reaction for online monitoring. Rather than conventional NMR spectroscopy experiments that rely on the use of deuterated water, the benchtop setting allows working in protonated solvents, and tailored water suppression techniques were used to make quantification more accurate. For the hydrolysis reaction, a 10% sucrose solution was hydrolyzed. The kinetic constants determined by the fractional conversion model were comparable to the results obtained in other studies. Quantitative online NMR spectroscopy can be considered as a promising tool for monitoring food processes in a continuous mode.

Effect of sucralose on the enzyme kinetics of invertase using real-time NMR spectroscopy and progress curve analysis

Sucralose, a derivative of sucrose, is widely used in noncaloric artificial sweeteners (NAS). Contrary to the belief that sucralose is physiologically inert and a healthy alternative sweetener to natural sugar, emerging studies indicate that sucralose alters the host metabolism as well as the composition of the microbiome. In this manuscript, we use real-time nuclear magnetic resonance (NMR) spectroscopy to demonstrate that sucralose alters the enzymatic conversion of sucrose to glucose and fructose. The real-time NMR progress curve analysis suggests that sucralose has the characteristic of a competitive inhibitor on the kinetics of the enzymatic process. This affects the rate of glucose production, and thus indirectly affecting the mutarotation process of α-D-glucose to β-D-glucose conversion. At a 1:2 M ratio of sucrose to sucralose, the results show that the catalytic efficiency of the enzyme is reduced by more than 50% in comparison to the measurements without sucralose. Altogether, as sucralose alters the rate of glucose production, sucralose cannot be considered inert to the metabolism as several downstream events in both prokaryotic and eukaryotic systems strongly depend on the rate of glucose metabolism.

Desktop NMR spectroscopy for real-time monitoring of an acetalization reaction in comparison with gas chromatography and NMR at 9.4T.

Monitoring of chemical reactions in real-time is in demand for process control. Different methods such as gas chromatography (GC), mass spectroscopy, infrared spectroscopy, and nuclear magnetic resonance (NMR) are used for that purpose. The current state-of-the-art compact NMR systems provide a useful method to employ with various reaction conditions for studying chemical reactions inside the fume hood at the chemical workplace. In the present study, an acetalization reaction was investigated with compact NMR spectroscopy in real-time. Acetalization is used for multistep synthesis of the variety of organic compounds to protect particular chemical groups. A compact 1T NMR spectrometer with a permanent magnet was employed to monitor the acid catalyzed acetalization of the p-nitrobenzaldehyde with ethylene glycol. The concentrations of both reactant and product were followed by peak integrals in single-scan 1H NMR spectra as a function of time. The reaction conditions were varied in terms of temperature, agitation speed, catalyst loading, and feed concentrations in order to determine the activation energy with the help of a pseudo-homogeneous kinetic model. For low molar ratios of aldehyde and glycol, the equilibrium conversions were lower than for the stoichiometric ratio. Increasing catalyst concentration leads to faster conversion. The data obtained with low-field NMR spectroscopy were compared with data from GC and NMR spectroscopy at 9.4T acquired in batch mode by extracting samples at regular time intervals. The reaction kinetics followed by either method agreed well. The activation energies for forward and backward reactions were determined by real-time monitoring with compact NMR at 1T were 48±5 and 60±4kJ/mol, respectively. The activation energies obtained with gas chromatography for forward and backward reactions were 48±4 and 51±4kJ/mol. The equilibrium constant decreases with increasing temperature as expected for an exothermic reaction. The impact of dense sampling with online NMR and sparse sampling with GC was observed on the kinetic outcome using the same kinetic model. Graphical abstract Acetalization reaction kinetics were monitored with real-time desktop NMR spectroscopy at 1T. Each data point was obtained at regular intervals with a single shot in 15s. The kinetics was compared with sparsely sampled data obtained with GC and NMR at 9.4T.

Cell-Free Protein Synthesis Enhancement from Real-Time NMR Metabolite Kinetics: Redirecting Energy Fluxes in Hybrid RRL Systems.

A counterintuitive cell-free protein synthesis (CFPS) strategy, based on reducing the ribosomal fraction in rabbit reticulocyte lysate (RRL), triggers the development of hybrid systems composed of RRL ribosome-free supernatant complemented with ribosomes from different mammalian cell-types. Hybrid RRL systems maintain translational properties of the original ribosome cell types, and deliver protein expression levels similar to RRL. Here, we show that persistent ribosome-associated metabolic activity consuming ATP is a major obstacle for maximal protein yield. We provide a detailed picture of hybrid CFPS systems energetic metabolism based on real-time nuclear magnetic resonance (NMR) investigation of metabolites kinetics. We demonstrate that protein synthesis capacity has an upper limit at native ribosome concentration and that lower amounts of the ribosomal fraction optimize energy fluxes toward protein translation, consequently increasing CFPS yield. These results provide a rationalized strategy for further mammalian CFPS developments and reveal the potential of real-time NMR metabolism phenotyping for optimization of cell-free protein expression systems.

Two UDP-glucuronic acid decarboxylases involved in the biosynthesis of a bacterial exopolysaccharide in Paenibacillus elgii.

Xylose is described as a component of bacterial exopolysaccharides in only a limited number of bacterial strains. A bacterial strain, Paenibacillus elgii, B69 was shown to be efficient in producing a xylose-containing exopolysaccharide. Sequence analysis was performed to identify the genes encoding the uridine diphosphate (UDP)-glucuronic acid decarboxylase required for the synthesis of UDP-xylose, the precursor of the exopolysaccharide. Two sequences, designated as Peuxs1 and Peuxs2, were found as the candidate genes for such enzymes. The activities of the UDP-glucuronic acid decarboxylases were proven by heterologous expression and real-time nuclear magnetic resonance analysis. The intracellular activity and effect of these genes on the synthesis of exopolysaccharide were further investigated by developing a thymidylate synthase based knockout system. This system was used to substitute the conventional antibiotic resistance gene system in P. elgii, a natural multi-antibiotic resistant strain. Results of intracellular nucleotide sugar analysis showed that the intracellular UDP-xylose and UDP-glucuronic acid levels were affected in Peuxs1 or Peuxs2 knockout strains. The knockout of either Peuxs1 or Peuxs2 reduced the polysaccharide production and changed the monosaccharide ratio. No polysaccharide was found in the Peuxs1/Peuxs2 double knockout strain. Our results show that P. elgii can be efficient in forming UDP-xylose, which is then used for the synthesis of xylose-containing exopolysaccharide.