Decarboxylation Pathway Research Articles

De Novo Biosynthesis of Glutarate via α-Keto Acid Carbon Chain Extension and Decarboxylation Pathway in Escherichia coli.

Microbial based bioplastics are promising alternatives to petroleum based synthetic plastics due to their renewability and economic feasibility. Glutarate is one of the most potential building blocks for bioplastics. The recent biosynthetic routes for glutarate were mostly based on the l-lysine degradation pathway from Pseudomonas putida that required lysine either by feeding or lysine overproduction via genetic manipulations. Herein, we established a novel glutarate biosynthetic pathway by incorporation of a "+1" carbon chain extension pathway from α-ketoglutarate (α-KG) in combination with α-keto acid decarboxylation pathway in Escherichia coli. Introduction of homocitrate synthase (HCS), homoaconitase (HA) and homoisocitrate dehydrogenase (HICDH) from Saccharomyces cerevisiae into E.coli enabled "+1" carbon extension from α-KG to α-ketoadipate (α-KA), which was subsequently converted into glutarate by a promiscuous α-keto acid decarboxylase (KivD) and a succinate semialdehyde dehydrogenase (GabD). The recombinant E.coli coexpressing all five genes produced 0.3 g/L glutarate from glucose. To further improve the titers, α-KG was rechanneled into carbon chain extension pathway via the clustered regularly interspersed palindromic repeats system mediated interference (CRISPRi) of essential genes sucA and sucB in tricarboxylic acid (TCA) cycle. The final strain could produce 0.42 g/L glutarate, which was increased by 40% compared with the parental strain.

Surface-termination dependence of propanoic acid deoxygenation on Mo2C

Although Mo2C is used as an alternative catalyst material for biomass conversion, the dependence of its reaction on the type of surface termination has not been studied. In the present study, we performed density functional theory calculations for the deoxygenation of propanoic acid on the two types of surface terminations possible for orthorhombic Mo2C (100), namely, on Mo- and C-terminated surfaces. The reaction energetics of the three possible deoxygenation pathways, namely, those for hydrodeoxygenation, decarbonylation, and decarboxylation, were compared by calculating the activation energies for their key surface reactions, such as hydrogenation and the scission of CC, CO, and OH bonds. The Mo-terminated surface was advantageous in the case of the hydrodeoxygenation pathway because of its low kinetic energy barrier for the hydrogenation of the oxygen species, while the C-terminated surface preferred the decarboxylation pathway because of its low kinetic energy barrier for OH bond scission.

Mechanisms and Origins of Chemo- and Regioselectivities of Ru(II)-Catalyzed Decarboxylative C-H Alkenylation of Aryl Carboxylic Acids with Alkynes: A Computational Study.

The mechanisms and chemo- and regioselectivities of Ru(II)-catalyzed decarboxylative C-H alkenylation of aryl carboxylic acids with alkynes were investigated with density functional theory (DFT) calculations. The catalytic cycle involves sequential carboxylate-directed C-H activation, alkyne insertion, decarboxylation and protonation. The facile tether-assisted decarboxylation step directs the intermediate toward the desired decarboxylative alkenylation, instead of typical annulation and double alkenylation pathways. The decarboxylation barrier is very sensitive to the tether length, and only the seven-membered ring intermediate can selectively undergo the designed decarboxylation, suggesting a tether-dependent chemoselectivity. This tether-dependent chemoselectivity also applies to the alkyl tethers. In addition, the polarity of solvent is found to control the chemoselectivity between the decarboxylative alkenylation and [4 + 2] annulation. Solvent with low polarity (toluene) favors the decarboxylation pathway, leading to the decarboxylative alkenylation. Solvent with high polarity (methanol) favors the ionic stepwise C-O reductive elimination pathway, leading to the [4 + 2] annulation. To understand the origins of regioselectivity with asymmetric alkynes, the distortion/interaction analysis was applied to the alkyne insertion transition states, and led to a predictive frontier molecular orbital model. The asymmetric alkynes selectively use the terminal with the larger HOMO orbital coefficient to form the C-C bond in the insertion step.

Methanol Steam Reforming: Na Doping of Pt/YSZ Provides Fine Tuning of Selectivity

In this work, we found that sodium doping can be used to improve CO2 selectivity for supported Pt catalyst during methanol steam reforming. These materials are usually very active in the low temperature range; however, they are characterized by high selectivity of CO, which is a poison in downstream polymer electrolyte membrane fuel cells (PEM-FC) application. With Na doping, we found that CO2 selectivity was higher than 90% when 2.5 wt.% of sodium was added to Pt/YSZ. We have speculated that the different product distribution is due to a different reaction pathway being opened for CH3OH decomposition. Methanol decarbonylation was favored when Na was absent or low, while a formate decarboxylation pathway was favored when Na content reached 2.5 wt.%. The proposal is rooted in the observed weakening of the C-H bond of formate, as demonstrated in in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and kinetic isotope effect (KIE) experiments for the water-gas shift reaction conducted at low temperature. When adsorbed methoxy, produced when methanol is dissociatively adsorbed, was converted in the presence of H2O in DRIFTS spectroscopy, formate species were prevalent for a 2% Pt–2.5% Na/YSZ catalyst, while only a minor contribution was observed for 2% Pt/YSZ. Moreover, the formate produced on Na-doped Pt/YSZ exhibited ν(CH) stretching bands at low wavenumber, consistent with C–H bond weakening, thus favoring dehydrogenation (and decarboxylation). It is proposed that when Na is present, formate is likely an intermediate, and because its dehydrogenation is favored, selectivity can be fine-tuned between decarbonylation and decarboxylation based on Na dopant level.

Fatty acid decarboxylation reaction kinetics and pathway of co-conversion with amino acid on supported iron oxide catalysts

Reaction kinetics and pathways of palmitic acid decarboxylation on Fe2O3/Al-MCCM-41 catalyst.

Reductive Activation of O2 by Non-Heme Iron(II) Benzilate Complexes of N4 Ligands: Effect of Ligand Topology on the Reactivity of O2-Derived Oxidant.

A series of iron(II) benzilate complexes (1-7) with general formula [(L)FeII(benzilate)]+ have been isolated and characterized to study the effect of supporting ligand (L) on the reactivity of metal-based oxidant generated in the reaction with dioxygen. Five tripodal N4 ligands (tris(2-pyridylmethyl)amine (TPA in 1), tris(6-methyl-2-pyridylmethyl)amine (6-Me3-TPA in 2), N1,N1-dimethyl-N2,N2-bis(2-pyridylmethyl)ethane-1,2-diamine (iso-BPMEN in 3), N1,N1-dimethyl-N2,N2-bis(6-methyl-2-pyridylmethyl)ethane-1,2-diamine (6-Me2-iso-BPMEN in 4), and tris(2-benzimidazolylmethyl)amine (TBimA in 7)) along with two linear tetradentate amine ligands (N1,N2-dimethyl-N1,N2-bis(2-pyridylmethyl)ethane-1,2-diamine (BPMEN in 5) and N1,N2-dimethyl-N1,N2-bis(6-methyl-2-pyridylmethyl)ethane-1,2-diamine (6-Me2-BPMEN in 6)) were employed in the study. Single-crystal X-ray structural studies reveal that each of the complex cations of 1-3 and 5 contains a mononuclear six-coordinate iron(II) center coordinated by a monoanionic benzilate, whereas complex 7 contains a mononuclear five-coordinate iron(II) center. Benzilate binds to the iron center in a monodentate fashion via one of the carboxylate oxygens in 1 and 7, but it coordinates in a bidentate chelating mode through carboxylate oxygen and neutral hydroxy oxygen in 2, 3, and 5. All of the iron(II) complexes react with dioxygen to exhibit quantitative decarboxylation of benzilic acid to benzophenone. In the decarboxylation pathway, dioxygen becomes reduced on the iron center and the resulting iron-oxygen oxidant shows versatile reactivity. The oxidants are nucleophilic in nature and oxidize sulfide to sulfoxide and sulfone. Furthermore, complexes 2 and 4-6 react with alkenes to produce cis-diols in moderate yields with the incorporation of both the oxygen atoms of dioxygen. The oxygen atoms of the nucleophilic oxidants do not exchange with water. On the basis of interception studies, nucleophilic iron(II) hydroperoxides are proposed to generate in situ in the reaction pathways. The difference in reactivity of the complexes toward external substrates could be attributed to the geometry of the O2-derived iron-oxygen oxidant. DFT calculations suggest that, among all possible geometries and spin states, high-spin side-on iron(II) hydroperoxides are energetically favorable for the complexes of 6-Me3-TPA, 6-Me2-iso-BPMEN, BPMEN, and 6-Me2-BPMEN ligands, while high spin end-on iron(II) hydroperoxides are favorable for the complexes of TPA, iso-BPMEN, and TBimA ligands.

Synthesis of the 1,3,4‐Oxadiazole Core through Thermolysis of Geminal Diazides

The thermolysis of geminal diazides derived from acylacetate compounds is an efficient tool for the rapid construction of the 1,3,4‐oxadiazole core. While a broad range of ethyl esters undergoes smooth transformation to the desired heterocycles that contain the ester moiety in moderate to high yields, the analogous tert‐butyl esters give rise to the oxadiazoles with acyl groups, presumably through a pathway of decarboxylation followed by a new acyl transfer.

Improving the productivity of S-adenosyl-l-methionine by metabolic engineering in an industrial Saccharomyces cerevisiae strain

S-Adenosyl-l-methionine (SAM) is an important metabolite having prominent roles in treating various diseases. In order to improve the production of SAM, the regulation of three metabolic pathways involved in SAM biosynthesis were investigated in an industrial yeast strain ZJU001. GLC3 encoded glycogen-branching enzyme (GBE), SPE2 encoded SAM decarboxylase, as well as ERG4 and ERG6 encoded key enzymes in ergosterol biosynthesis, were knocked out in ZJU001 accordingly. The results indicated that blocking of either glycogen pathway or SAM decarboxylation pathway could improve the SAM accumulation significantly in ZJU001, while single disruption of either ERG4 or ERG6 gene had no obvious effect on SAM production. Moreover, the double mutant ZJU001-GS with deletion of both GLC3 and SPE2 genes was also constructed, which showed further improvement of SAM accumulation. Finally, SAM2 was overexpressed in ZJU001-GS to give the best SAM-producing recombinant strain ZJU001-GS-SAM2, in which 12.47g/L SAM was produced by following our developed pseudo-exponential fed-batch cultivation strategy, about 81.0% increase comparing to its parent strain ZJU001. The present work laid a solid base for large-scale SAM production with the industrial Saccharomyces cerevisiae strain.

Theoretical Study on Catalytic Pyrolysis of Benzoic Acid as a Coal-Based Model Compound

Benzoic acid (C6H5COOH) is selected as a coal-based model compound, and its catalytic pyrolysis mechanisms on ZnO, γ-Al2O3, CaO, and MgO catalysts are studied using density functional theory (DFT) compared to the non-catalytic pyrolysis mechanism. DFT calculation shows that the pyrolysis process of C6H5COOH in the gas phase occurs via the direct decarboxylation pathway (C6H5COOH → C6H6 + CO2) or the stepwise decarboxylation pathway (C6H5COOH → C6H6COO → C6H6 + CO2). For C6H5COOH catalytic pyrolysis on the ZnO (1010) surface, the preferred reaction pathway is C6H5COOH → C6H5COO + H → C6H6 + CO2, whereas the preferred reaction pathway on γ-Al2O3 (110), CaO (100), and MgO (100) surfaces is C6H5COOH → C6H5COO + H → C6H5 + CO2 + H → C6H6 + CO2, indicating that the presence of catalysts changed the pyrolysis mechanism of C6H5COOH. In addition, dissociative adsorption of C6H5COOH is observed on these surfaces. It is found that ZnO (1010), MgO (100), and CaO (100) are beneficial to C6H5COOH decomposition, but γ...

Engineering Escherichia coli for Microbial Production of Butanone.

To expand the chemical and molecular diversity of biotransformation using whole-cell biocatalysts, we genetically engineered a pathway in Escherichia coli for heterologous production of butanone, an important commodity ketone. First, a 1-propanol-producing E. coli host strain with its sleeping beauty mutase (Sbm) operon being activated was used to increase the pool of propionyl-coenzyme A (propionyl-CoA). Subsequently, molecular heterofusion of propionyl-CoA and acetyl-CoA was conducted to yield 3-ketovaleryl-CoA via a CoA-dependent elongation pathway. Lastly, 3-ketovaleryl-CoA was channeled into the clostridial acetone formation pathway for thioester hydrolysis and subsequent decarboxylation to form butanone. Biochemical, genetic, and metabolic factors affecting relative levels of ketogenesis, acidogenesis, and alcohol genesis under selected fermentative culture conditions were investigated. Using the engineered E. coli strain for batch cultivation with 30 g liter(-1)glycerol as the carbon source, we achieved coproduction of 1.3 g liter(-1)butanone and 2.9 g liter(-1)acetone. The results suggest that approximately 42% of spent glycerol was utilized for ketone biosynthesis, and thus they demonstrate potential industrial applicability of this microbial platform.

ChemInform Abstract: Palladium‐Catalyzed Double‐Decarboxylative Addition to Pyrones: Synthesis of Conjugated Dienoic Esters.

An interceptive decarboxylative allylation protocol has been developed utilizing pyrone as a C4 synthon. This palladium-catalyzed transformation difunctionalizes the pyrone moiety by in situ generation and activation of both the electrophile and nucleophile via a double decarboxylation pathway. Ultimately, allyl carbonates react smoothly with 2-carboxypyrone under mild reaction conditions to generate synthetically useful acyclic dienoic esters, forming carbon dioxide as the sole byproduct.

Solvation Effects in the Hydrodeoxygenation of Propanoic Acid over a Model Pd(211) Catalyst

The effects of liquid water and 1,4-dioxane on the hydrodeoxygenation of propionic acid over Pd(211) model surfaces have been studied from first principles. A microkinetic model with parameters obtained from density functional theory and implicit solvation models was developed to study the effects of these solvents on the reaction mechanism and kinetic parameters. In the presence of water, dehydrogenated derivatives of propionic acid and propionate are stabilized, and a new decarboxylation mechanism involving CH3CCOOH surface species is facilitated, leading to a higher decarboxylation rate. However, stronger adsorption of CO in the presence of liquid water resulted in fewer free sites and an overall lower turnover frequency. By contrast, in the presence of 1,4-dioxane, the most dominant decarboxylation pathway does not involve a dehydrogenated propionate species, but propionate goes through decarboxylation to form CO2 and C2 fragments very similar to the mechanism in the gas phase. Again, in the presence ...

Solvent effects in the liquid phase hydrodeoxygenation of methyl propionate over a Pd(1 1 1) catalyst model

Solvation effects of liquid water and 1,4-dioxane have been studied from first principles for the hydrodeoxygenation of methyl propionate over a Pd(111) catalyst surface model. Microkinetic reaction models have been developed for various reaction environments to study the effects of solvents on the reaction mechanism. Our models predict that in all reaction environments, decarbonylation pathways are favored over decarboxylation pathways. However, in the presence of liquid water the decarboxylation mechanism is facilitated due to solvent stabilization of the dehydrogenated derivatives of propionate. Overall, the activity of Pd(111) is one order of magnitude lower in water than in 1,4-dioxane where we predict the activity to be very similar to the vapor phase. The decrease in Pd(111) activity due to liquid water can be traced back to the Pd surface being more crowded and propanoyl–methoxy type dissociations becoming more difficult. Propanoyl–methoxy type dissociations also become more rate controlling in liquid water than the dehydrogenation steps that are most rate controlling in 1,4-dioxane and in the vapor phase.

Palladium-Catalyzed Double-Decarboxylative Addition to Pyrones: Synthesis of Conjugated Dienoic Esters.

An interceptive decarboxylative allylation protocol has been developed utilizing pyrone as a C4 synthon. This palladium-catalyzed transformation difunctionalizes the pyrone moiety by in situ generation and activation of both the electrophile and nucleophile via a double decarboxylation pathway. Ultimately, allyl carbonates react smoothly with 2-carboxypyrone under mild reaction conditions to generate synthetically useful acyclic dienoic esters, forming carbon dioxide as the sole byproduct.

Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal alkene production

Biological production of terminal alkenes has garnered a significant interest due to their industrial applications such as lubricants, detergents and fuels. Here, we engineered the yeast Saccharomyces cerevisiae to produce terminal alkenes via a one-step fatty acid decarboxylation pathway and improved the alkene production using combinatorial engineering strategies. In brief, we first characterized eight fatty acid decarboxylases to enable and enhance alkene production. We then increased the production titer 7-fold by improving the availability of the precursor fatty acids. We additionally increased the titer about 5-fold through genetic cofactor engineering and gene expression tuning in rich medium. Lastly, we further improved the titer 1.8-fold to 3.7mg/L by optimizing the culturing conditions in bioreactors. This study represents the first report of terminal alkene biosynthesis in S. cerevisiae, and the abovementioned combinatorial engineering approaches collectively increased the titer 67.4-fold. We envision that these approaches could provide insights into devising engineering strategies to improve the production of fatty acid-derived biochemicals in S. cerevisiae.

The production of renewable transportation fuel through fed-batch and continuous deoxygenation of vegetable oil derived fatty acids over Pd/C catalyst

Renewable fuels such as green diesel from renewable biomass have received attentions because of energy and environmental concerns. Deoxygenation, used to upgrade biomass derived oils has been applied intensively nowadays. To successfully improve this process, fed-batch and following continuous processes on real biomass derived fatty acids need to be investigated. In this study, liquid-phase deoxygenation of vegetable oil derived fatty acids was carried out over 5% Pd/C with cofeeding H2. With sufficient hydrogen, complete hydrogenation of unsaturated fatty acids occurred, leading to successive deoxygenation of the saturated fatty acids with n-alkane yields of 99% and 88% and average CO2 selectivity of 94.9% and 94.6% in the fed-batch and continuous mode, respectively. After hydrogenation is completed, lower than 5% of effective H2 partial pressure was found to be favorable for the decarboxylation pathway and ideal for deoxygenation of biomass derived fatty acids. Copyright © 2015 John Wiley & Sons, Ltd.

Inactivation of agmatinase expressed in vegetative cells alters arginine catabolism and prevents diazotrophic growth in the heterocyst-forming cyanobacterium Anabaena.

Arginine decarboxylase produces agmatine, and arginase and agmatinase are ureohydrolases that catalyze the production of ornithine and putrescine from arginine and agmatine, respectively, releasing urea. In the genome of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120, ORF alr2310 putatively encodes an ureohydrolase. Cells of Anabaena supplemented with [14C]arginine took up and catabolized this amino acid generating a set of labeled amino acids that included ornithine, proline, and glutamate. In an alr2310 deletion mutant, an agmatine spot appeared and labeled glutamate increased with respect to the wild type, suggesting that Alr2310 is an agmatinase rather than an arginase. As determined in cell-free extracts, agmatinase activity could be detected in the wild type but not in the mutant. Thus, alr2310 is the Anabaena speB gene encoding agmatinase. The Δalr2310 mutant accumulated large amounts of cyanophycin granule polypeptide, lacked nitrogenase activity, and did not grow diazotrophically. Growth tests in solid media showed that agmatine is inhibitory for Anabaena, especially under diazotrophic conditions, suggesting that growth of the mutant is inhibited by non-metabolized agmatine. Measurements of incorporation of radioactivity from [14C]leucine into macromolecules showed, however, a limited inhibition of protein synthesis in the Δalr2310 mutant. Analysis of an Anabaena strain producing an Alr2310-GFP (green fluorescent protein) fusion showed expression in vegetative cells but much less in heterocysts, implying compartmentalization of the arginine decarboxylation pathway in the diazotrophic filaments of this heterocyst-forming cyanobacterium.

Activation of persulfate by UV and Fe 2+ for the defluorination of perfluorooctanoic acid

Efficient defluorination of perfluorooctanoic acid (PFOA) was achieved by integrating UV irradiation and Fe 2+ activation of persulfate (S2O8 2- ). It was found that the UV-Fe 2+ , Fe 2+ -S2O8 2- , and UV-S2O8 2- processes caused defluorination efficiency of 6.4%, 1.6% and 23.2% for PFOA at pH 5.0 within 5 h, respectively, but a combined system of UV-Fe 2+ -S2O8 2- dramatically promoted the defluorination efficiency up to 63.3%. The beneficial synergistic behavior between Fe 2+ -S2O8 2- and UV-S2O8 2- was demonstrated to be dependent on Fe 2+ dosage, initial S2O8 2- concentration, and solution pH. The decomposition of PFOA resulted in generation of shorter-chain perfluorinated carboxylic acids (PFCAs), formic acid and fluoride ions. The generated PFCAs intermediates could be further defluorinated by adding supplementary Fe 2+ and, S2O8 2- and re-adjusting solution pH in later reaction stage. The much enhanced PFOA defluorination in the UV-Fe 2+ -S2O8 2- system was attributed to the fact that the simultaneous employment of UV light and Fe 2+ not only greatly enhanced the activation of S2O8 2- to form strong oxidizing sulfate radicals (SO4 •- ), but also provided an additional decarboxylation pathway caused by electron transfer from PFOA to in situ generated Fe 3+ .

The growth and survival of Mycobacterium smegmatis is enhanced by co-metabolism of atmospheric H2.

The soil bacterium Mycobacterium smegmatis is able to scavenge the trace concentrations of H2 present in the atmosphere, but the physiological function and importance of this activity is not understood. We have shown that atmospheric H2 oxidation in this organism depends on two phylogenetically and kinetically distinct high-affinity hydrogenases, Hyd1 (MSMEG_2262-2263) and Hyd2 (MSMEG_2720-2719). In this study, we explored the effect of deleting Hyd2 on cellular physiology by comparing the viability, energetics, transcriptomes, and metabolomes of wild-type vs. Δhyd2 cells. The long-term survival of the Δhyd2 mutant was significantly reduced compared to the wild-type. The mutant additionally grew less efficiently in a range of conditions, most notably during metabolism of short-chain fatty acids; there was a twofold reduction in growth rate and growth yield of the Δhyd2 strain when acetate served as the sole carbon source. Hyd1 compensated for loss of Hyd2 when cells were grown in a high H2 atmosphere. Analysis of cellular parameters showed that Hyd2 was not necessary to generate the membrane potential, maintain intracellular pH homeostasis, or sustain redox balance. However, microarray analysis indicated that Δhyd2 cells were starved for reductant and compensated by rewiring central metabolism; transcripts encoding proteins responsible for oxidative decarboxylation pathways, the urea cycle, and ABC transporter-mediated import were significantly more abundant in the Δhyd2 mutant. Metabolome profiling consistently revealed an increase in intracellular amino acids in the Δhyd2 mutant. We propose that atmospheric H2 oxidation has two major roles in mycobacterial cells: to generate reductant during mixotrophic growth and to sustain the respiratory chain during dormancy.

ChemInform Abstract: Copper‐Mediated Oxidative Trifluoromethylthiolation of Aryl Boronic Acids with CF3CO2Na and Elemental Sulfur.

AbstractInexpensive sodium trifluoroacetate and elemental sulfur are employed as reagents to access aryl trifluoromethyl thioethers through an oxidative decarboxylative pathway.