Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil

A new lanthanide (Ln3+)-dependent methanol-utilizing bacterial strain, La3113T, was isolated from rice field soil and its taxonomic position was investigated using polyphasic approaches. The strain was aerobic, Gram-stain-negative, strongly motile, catalase-positive and cytochrome oxidase-positive. It could neither catalyse the hydrolysis of urea nor reduce nitrate to nitrite. Growth was observed within a temperature range of 10–40 °C and a pH range of 6–8, with optimum growth at 28 °C and pH 7. Methylamine was utilized as the single source of energy, carbon and nitrogen, and it was oxidized by methylamine dehydrogenase. C16 : 1 ω7c, C16 : 1 ω6c and C16 : 0 were the dominant cellular fatty acids. Its draft genome (2.67 Mbp and 44.9 mol% G+C content) encodes genes including three Ln3+-dependent methanol dehydrogenase (XoxF-type MDH) genes, those for formaldehyde assimilation (ribulose monophosphate pathway), formate dehydrogenases and methylamine dehydrogenases, but not Ca2+-dependent MDH (MxaFI-MDH), which characterizes the species as a Ln3+-dependent methylotroph. The 16S rRNA gene sequence showed that strain La3113T belongs to the genus Methylotenera and is closely related to Methylotenera mobilis JLW8T (98.29 % identity). The digital DNA–DNA hybridization (dDDH) values (less than 30 %) and average nucleotide identity (ANI) values (less than 85 %) between genomes of strain La3113T and related type strains were lower than the thresholds for species delineation (70 % for dDDH and 95–96 % for ANI). On the basis of these polyphasic approaches, we propose a novel Methylotenera species, Methylotenera oryzisoli sp. nov. (type strain La3113T=NBRC 111954T=DSM 103219T).

On the theory of time dilation in chemical kinetics

The rates of chemical reactions are not absolute but their magnitude depends upon the relative speeds of the moving observers. This has been proved by unifying basic theories of chemical kinetics, which are transition state theory, collision theory, RRKM and Marcus theory, with the special theory of relativity. Boltzmann constant and energy spacing between permitted quantum levels of molecules are quantum mechanically proved to be Lorentz variant. The relativistic statistical thermodynamics has been developed to explain quasi-equilibrium existing between reactants and activated complex. The newly formulated Lorentz transformation of the rate constant from Arrhenius equation, of the collision frequency and of the Eyring and Marcus equations renders the rate of reaction to be Lorentz variant. For a moving observer moving at fractions of the speed of light along the reaction coordinate, the transition state possess less kinetic energy to sweep translation over it. This results in the slower transformation of reactants into products and in a stretched time frame for the chemical reaction to complete. Lorentz transformation of the half-life equation explains time dilation of the half-life period of chemical reactions and proves special theory of relativity and presents theory in accord with each other. To demonstrate the effectiveness of the present theory, the enzymatic reaction of methylamine dehydrogenase and radioactive disintegration of Astatine into Bismuth are considered as numerical examples.

Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria

ABSTRACT The C1-compound monomethylamine can serve as a nitrogen, carbon, and energy source for heterotrophic bacteria. The marine alphaproteobacterium Donghicola sp. strain KarMa can use monomethylamine as a source only for nitrogen and not for carbon. Its draft genome sequence is presented here and reveals putative gene clusters for the methylamine dehydrogenase and the N-methylglutamate pathways for monomethylamine metabolism.

Draft Genome Sequence of Methylophaga muralis Bur 1, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph Isolated from a Soda Lake

The draft genome sequence of Methylophaga muralis strain Bur 1 (VKM B-3046T), a non-methane-utilizing methylotroph isolated from a soda lake, is reported here. Strain Bur 1 possesses genes for methanol and methylamine (methylamine dehydrogenase and N-methylglutamate pathway) oxidation. Genes for the biosynthesis of ectoine were also found.

MauG catalysis: a tale of ferryl iron, radicals and long distance hopping

Methylamine dehydrogenase (MADH) enables some methylotrophic/autotrophic bacteria to grow on methylamine as a sole source of carbon and energy. MADH catalysis depends on the cofactor tryptophan tryptophylquinone (TTQ) that is a posttranslational modification of two Trp residues in the MADH β-subunit. The maturation of MADH depends on four gene products located in the methylamine utilization (mau) gene cluster. One of these, mauG, encodes a c-type di-heme enzyme that completes synthesis of the TTQ cofactor. The potent oxidant is an unusual bis-Fe(IV) MauG species composed of a ferryl heme (Fe(IV)=O) with an oxidizing equivalent stored as Fe(IV) at the second heme, which has an unusual His, Tyr axial ligation. The bis-Fe(IV) oxidant is formally Fe(V) and equivalent to Compound I. Completion of TTQ to generate active MADH involves long-range electron transfer and a radical hopping mechanism to effect catalysis over a 40 Å distance. The MauG catalyzed reaction occurs in three discrete 2-electron events in a hydrogen peroxide or molecular oxygen (+ reducing equivalents) dependent process. A crystal structure of MauG in complex with its protein substrate, a precursor form of MADH known as preMADH, has been solved. The crystals are catalytically active. The order of the 2-electron chemistry catalyzed by MauG was determined through a series of structures from crystals harvested after different amounts of time following crystallization. Hydrogen peroxide to initiate the reaction was generated by the slow breakdown of polyethylene glycol used in crystallization. These in crystallo data are corroborated by mass spectrometry in solution experiments.

Investigation of the molecular mechanisms of electronic decoherence within a quinone cofactor

The notion of decoherence is particularly adapted to discuss the quantum-to-classical transition in the context of chemical reactions. Decoherence can be modeled by computing the time evolution of nuclear wave packets evolving on distinct potential energy surfaces, here using density functional theory (DFT) and Born–Oppenheimer molecular dynamics simulations. We investigate a redox cofactor of biological interest (tryptophan tryptophylquinone, TTQ) found in the enzyme methylamine dehydrogenase. We also report the first systematic comparison of semi-empirical DFT (tight-binding DFT) and classical force field approaches for estimating decoherence in molecular systems. In the TTQ cofactor, we find that decoherence combines structural and dynamical aspects: it is initiated by the divergent motions of few atoms and then propagates dynamically to the remaining atoms. It is the mass effect of all the atoms that leads to decoherence within a few femtosecond.