Endophytic fungi are rich sources of structurally complex chemical scaffolds with interesting biological activities. However, their metabolome is still unknown, making them appealing for novel compound discovery. To maximize the number of secondary metabolites produced from a single microbial source, we used the "OSMAC (one strain-many compounds) approach." In potato dextrose medium, M. phaseolina produced phomeolic acid (1), ergosterol peroxide (2), and a volatile compound 1,4-benzene-diol. Incorporating an epigenetic modifier, sodium valproate, affected the metabolite profile of the fungus. It produced 3-acetyl-3-methyl dihydro-furan-2(3H)-one (3) and methyl-2-(methyl-thio)-butyrate (4), plus volatile chemicals: butylated hydroxy toluene (BHT), di-methyl-formamide, 3-amino-1-propanol, and 1,4-benzenediol, 2-amino-1-(O-methoxyphenyl) propane. The structure of compounds 1-4 was established with the help of spectroscopic data. This study revealed first-time compounds 1-4 in the fungus M. phaseolina using a classical and epigenetic manipulation approach.
- MeSH
- Ascomycota * metabolism MeSH
- Benzene metabolism MeSH
- Brugmansia * MeSH
- Butylated Hydroxytoluene metabolism MeSH
- Butyrates metabolism MeSH
- Endophytes chemistry MeSH
- Epigenesis, Genetic MeSH
- Formamides metabolism MeSH
- Furans metabolism MeSH
- Glucose metabolism MeSH
- Valproic Acid metabolism MeSH
- Propane metabolism MeSH
- Toluene metabolism MeSH
- Publication type
- Journal Article MeSH
Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.
- MeSH
- Formamides chemistry MeSH
- Prebiotics analysis MeSH
- Origin of Life MeSH
- Thymine chemistry MeSH
- Uracil chemistry MeSH
- Publication type
- Journal Article MeSH
The Miller-Urey experiments pioneered modern research on the molecular origins of life, but their actual relevance in this field was later questioned because the gas mixture used in their research is considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the production of only amino acids has been taken as evidence of the limited relevance of the results. Here, we report an experimental work, combined with state-of-the-art computational methods, in which both electric discharge and laser-driven plasma impact simulations were carried out in a reducing atmosphere containing NH3 + CO. We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results.
The end of the late heavy bombardment era coincides with the emergence of life on the Earth 4 billion years ago. This coincidence suggests that the impacts of extraterrestrial bodies might have contributed to the formation of the first molecules involved in early living structures. We have simulated a high-energy synthesis of nucleic acid bases from formamide in the impact of an extraterrestrial body. The high-power laser system PALS was employed in simulation of impact plasma by inducing a laser dielectric breakdown in formamide. In hot and dense plasma, formamide decomposed producing reactive radicals. The radicals reacted with formamide and nucleic acid bases were produced. Formamide was pretreated with laser plasma in the presence of catalysts. The products were analyzed by FTIR spectrometry and GC-MS. Time-resolved emission spectra of formamide discharge plasma were measured. Kinetic models and formation pathways for nucleic acid bases were calculated. The results show that the nucleic acid bases can be synthesized in impact plasma involving CN and NH radicals and formamide.
The effect of non-denaturing concentrations of three different organic solvents, formamide, acetone and isopropanol, on the structure of haloalkane dehalogenases DhaA, LinB, and DbjA at the protein-solvent interface was studied using molecular dynamics simulations. Analysis of B-factors revealed that the presence of a given organic solvent mainly affects the dynamical behavior of the specificity-determining cap domain, with the exception of DbjA in acetone. Orientation of organic solvent molecules on the protein surface during the simulations was clearly dependent on their interaction with hydrophobic or hydrophilic surface patches, and the simulations suggest that the behavior of studied organic solvents in the vicinity of hyrophobic patches on the surface is similar to the air/water interface. DbjA was the only dimeric enzyme among studied haloalkane dehalogenases and provided an opportunity to explore effects of organic solvents on the quaternary structure. Penetration and trapping of organic solvents in the network of interactions between both monomers depends on the physico-chemical properties of the organic solvents. Consequently, both monomers of this enzyme oscillate differently in different organic solvents. With the exception of LinB in acetone, the structures of studied enzymes were stabilized in water-miscible organic solvents.
- MeSH
- 2-Propanol chemistry pharmacology MeSH
- Acetone chemistry pharmacology MeSH
- Formamides chemistry pharmacology MeSH
- Hydrophobic and Hydrophilic Interactions MeSH
- Hydrolases chemistry MeSH
- Crystallography, X-Ray MeSH
- Protein Structure, Quaternary drug effects MeSH
- Models, Molecular MeSH
- Solvents chemistry MeSH
- Molecular Dynamics Simulation MeSH
- Protein Structure, Tertiary drug effects MeSH
- Water chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection of the cosolvent type and concentration range for an enzymatic reaction is challenging and requires extensive empirical testing. An understanding of protein-solvent interaction could provide a theoretical framework for rationalising the selection process. Here, the behaviour of three model enzymes (haloalkane dehalogenases) was investigated in the presence of three representative organic cosolvents (acetone, formamide, and isopropanol). Steady-state kinetics assays, molecular dynamics simulations, and time-resolved fluorescence spectroscopy were used to elucidate the molecular mechanisms of enzyme-solvent interactions. Cosolvent molecules entered the enzymes' access tunnels and active sites, enlarged their volumes with no change in overall protein structure, but surprisingly did not act as competitive inhibitors. At low concentrations, the cosolvents either enhanced catalysis by lowering K(0.5) and increasing k(cat), or caused enzyme inactivation by promoting substrate inhibition and decreasing k(cat). The induced activation and inhibition of the enzymes correlated with expansion of the active-site pockets and their occupancy by cosolvent molecules. The study demonstrates that quantitative analysis of the proportions of the access tunnels and active-sites occupied by organic solvent molecules provides the valuable information for rational selection of appropriate protein-solvent pair and effective cosolvent concentration.
- MeSH
- 2-Propanol chemistry metabolism MeSH
- Acetone chemistry metabolism MeSH
- Time Factors MeSH
- Spectrometry, Fluorescence MeSH
- Formamides chemistry metabolism MeSH
- Hydrolases chemistry metabolism MeSH
- Catalytic Domain MeSH
- Kinetics MeSH
- Solvents chemistry metabolism MeSH
- Molecular Dynamics Simulation MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Metabolism of the solvents N,N-dimethylformamide (DMF) and N-methylformamide (MF) results in the formation of N-methylcarbamoyl adducts at the N-terminal valine and lysine in blood protein globin, of which the lysine adduct has so far only been reported in rats given high doses of both solvents [Mráz, J., Simek, P., Chvalová, D., Nohová, H., Smigolová, P., 2004. Studies on the methyl isocyanate adducts in globin. Chem. Biol. Interact. 148, 1-10]. Here we examined whether the lysine adduct is produced, and accessible to analysis, in humans occupationally or experimentally exposed to DMF. Globin from exposed subjects (n=35) and unexposed controls (n=5) was analyzed by two methods. Edman degradation was used as a sensitive reference method to measure the valine adduct by converting it to 3-methyl-5-isopropylhydantoin (MVH). The MVH levels in globin of the exposed subjects were in the range of 1-441 nmol/g, in controls <1 nmol/g. The principal method of globin analysis consisted of enzymatic hydrolysis with pronase to release free N(epsilon)-(N-methylcarbamoyl)lysine (MLU) and N-methylcarbamoylvaline (MVU), which were determined by HPLC/MS/MS, with no clean-up or preconcentration steps needed. For MLU, the parent and product ions were m/z 204-->173, and the limit of detection was approximately 5 nmol/g globin. MLU was found in most globins from the exposed subjects but not in the controls. A close correlation between the MLU and MVH levels (nmol/g) was observed: MLU=7+0.48 MVH (R(2)=0.84, n=32). In conclusion, MLU can be easily measured in globin of workers exposed to DMF. The findings also indicate a long-term persistence of MLU in the human body, and consequently, its potential as a biomarker of chronic exposure to DMF.
