Intermediate-assisted multifunctional catalysis in the conversion of flavin to 5,6-dimethylbenzimidazole by BluB: a density functional theory study

The coenzyme B12 precursor 5,6-dimethylbenzimidazole is a flavin antagonist in Salmonella

Salmonella enterica subsp. enterica sv. Typhimurium str. LT2 (hereafter S. Typhimurium) synthesizes adenosylcobalamin (AdoCbl, CoB12) de novo only under anoxic conditions, but it can assemble the lower ligand loop (a.k.a. the nucleotide loop) and can form the unique C-Co bond present in CoB12 in the presence or absence of molecular oxygen. During studies of nucleotide loop assembly in S. Typhimurium, we noticed that the growth of this bacterium could be arrested by the lower ligand nucleobase, namely 5,6-dimethylbenzimidazole (DMB). Here we report in vitro and in vivo evidence that shows that the structural similarity of DMB to the isoalloxazine moiety of flavin cofactors causes its deleterious effect on cell growth. We studied DMB inhibition of the housekeeping flavin dehydrogenase (Fre) and three flavoenzymes that initiate the catabolism of tricarballylate, succinate or D-alanine in S. Typhimurium. Notably, while growth with tricarballylate was inhibited by 5-methyl-benzimidazole (5-Me-Bza) and DMB, growth with succinate or glycerol was arrested by DMB but not by 5-Me-Bza. Neither unsubstituted benzimidazole nor adenine inhibited growth of S. Typhimurium at DMB inhibitory concentrations. Whole genome sequencing analysis of spontaneous mutant strains that grew in the presence of inhibitory concentrations of DMB identified mutations effecting the cycA (encodes D-Ala/D-Ser transporter) and dctA (encodes dicarboxylate transporter) genes and in the coding sequence of the tricarballylate transporter (TcuC), suggesting that increased uptake of substrates relieved DMB inhibition. We discuss two possible mechanisms of inhibition by DMB.

Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates-Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid

The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O2 to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. Nevertheless, the spin-forbidden addition of O2 to uncharged ligands has also been observed in the laboratory, and the detailed mechanism of how the system circumvents the spin-forbiddenness of the reaction is still unknown. One of these examples is the cofactorless peroxidation of 2-methyl-3,4-dihydro-1-naphthol, which will be studied computationally using single and multi-reference electronic structure calculations. Our results show that the preferred mechanism is that in which O2 picks a proton from the substrate in the triplet state, and subsequently hops to the singlet state in which the product is stable. For this reaction, the formation of the radical pair is associated with a higher barrier than that associated with the intersystem crossing, even though the absence of the negative charge leads to relatively small values of the spin-orbit coupling.

Comparative Metabolic Responses Induced by Pyridine and Imidazole in Blakeslea trispora

Lycopene cyclase needs to be inhibited by the blockers like pyridine or imidazole in the lycopene accumulation of Blakeslea trispora. This work investigated how pyridine and imidazole impacted the basal metabolism of B. trispora, the results helped us understand how they could affect the lycopene production and application, and see the metabolic risks from different inhibitors. In this study, the highest yield of lycopene with pyridine was obtained at 176 mg/L without amino acids supplement, and got more lycopene at 237 mg/L adding tyrosine, lysine, proline all together as 0.01 mol/L each in fermented broth. GC-MS and Principal Component Analysis (PCA) were used to find that amino acids, fatty acids, organic acids including phosphoric acid, carbon source and imidazole derivatives played the most important roles in lycopene fermentation with imidazole, differently, fatty acids, carbon source, and pyridine derivatives were more significant in the pyridine process and it was remarkable that the residual of both blockers' derivatives would bring the potential risks on applications of lycopene products. Predominantly, durene met 0.35 mg/g DCW with imidazole and piperidine formaldehyde attained 0.24 mg/g DCW with pyridine after the end of lycopene fermentations.

Unique Biochemical and Sequence Features Enable BluB To Destroy Flavin and Distinguish BluB from the Flavin Monooxygenase Superfamily

Vitamin B₁₂ (cobalamin) is an essential micronutrient for humans that is synthesized by only a subset of bacteria and archaea. The aerobic biosynthesis of 5,6-dimethylbenzimidazole, the lower axial ligand of cobalamin, is catalyzed by the "flavin destructase" enzyme BluB, which fragments reduced flavin mononucleotide following its reaction with oxygen to yield this ligand. BluB is similar in sequence and structure to members of the flavin oxidoreductase superfamily, yet the flavin destruction process has remained elusive. Using stopped-flow spectrophotometry, we find that the flavin destructase reaction of BluB from Sinorhizobium meliloti is initiated with canonical flavin-O₂ chemistry. A C4a-peroxyflavin intermediate is rapidly formed in BluB upon reaction with O₂, and has properties similar to those of flavin-dependent hydroxylases. Analysis of reaction mixtures containing flavin analogues indicates that both formation of the C4a-peroxyflavin and the subsequent destruction of the flavin to form 5,6-dimethylbenzimidazole are influenced by the electronic properties of the flavin isoalloxazine ring. The flavin destruction phase of the reaction, which results from the decay of the C4a-peroxyflavin intermediate, occurs more efficiently at pH >7.5. Furthermore, the BluB mutants D32N and S167G are specifically impaired in the flavin destruction phase of the reaction; nevertheless, both form the C4a-peroxyflavin nearly quantitatively. Coupled with a phylogenetic analysis of BluB and related flavin-dependent enzymes, these results demonstrate that the BluB flavin destructase family can be identified by the presence of active site residues D32 and S167.

Catalytic Amine Oxidation under Ambient Aerobic Conditions: Mimicry of Monoamine Oxidase B

The flavoenzyme monoamine oxidase (MAO) regulates mammalian behavioral patterns by modulating neurotransmitters such as adrenaline and serotonin. The mechanistic basis which underpins this enzyme is far from agreed upon. Reported herein is that the combination of a synthetic flavin and alloxan generates a catalyst system which facilitates biomimetic amine oxidation. Mechanistic and electron paramagnetic (EPR) spectroscopic data supports the conclusion that the reaction proceeds through a radical manifold. This data provides the first example of a biorelevant synthetic model for monoamine oxidase B activity.

Effect of stacking interactions on the thermodynamics and kinetics of lumiflavin: a study with improved density functionals and density functional tight-binding protocol

The π-π stacking interaction between lumiflavin and a number of π-electron-rich molecules has been studied by density functional theory using several new-generation density functionals. Six known lumiflavin-aromatic adducts were used and the models were evaluated by comparing the geometry and energetics with experimental results. The study found that dispersion-corrected and hybrid functionals with larger (>50%) Hartree-Fock exchanges produced superior results in modeling thermodynamic characteristics of these complexes. The functional producing the best energetics for these model systems was used to study the stacking interactions of lumiflavin with biologically relevant aromatic groups. Additionally, the reduction of flavin-in the presence of both a hydride donor and a nondonor π-electronic system was also studied. Weak interactions were observed in the stacked lumiflavin complexes of benzene, phenol, and indole, mimicking phenyl alanine, tryptophan, and tyrosine side chains, respectively, of an enzyme. The stacked complex of naphthalene and flavin showed little change in flavin's redox potential indicating insignificant effect on the thermodynamics of the hydride transfer reaction. In contrast, the hydride transfer reaction with the hydride donor N-methyl nicotinamide tells a different story, as the transition state was found to be strongly impacted by the stacking interactions. A comparison of performance between the density functional theory (DFT) and the computationally less expensive dispersion-corrected self-consistent density functional tight-binding (SCC-DFTB-D) theory revealed that the latter produces consistent energetics for this hydride transfer reaction and additional DFT-computed perturbative corrections could significantly improve these results.

Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae

The Roseobacter clade is a ubiquitous group of marine α-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae.

The oceans are home to a large variety of microorganisms, which interact in several ways with world-wide metabolic cycles. A representative of an important group of marine bacteria called the Roseobacter clade is Dinoroseobacter shibae. This organism is known to use a variant of photosynthesis to obtain energy from light. Another feature of D. shibae and many other Roseobacters is the ability to degrade an abundant compound in the ocean called dimethylsulfoniopropionate. Importantly, one degradation pathway of dimethylsulfoniopropionate releases a side product, which affects climate by seeding cloud formation. In this work, we constructed a genome-scale metabolic model of D. shibae and carried out a detailed computational analysis of its metabolism. Our model simulates the light-harvesting capabilities of D. shibae and also accounts for the energy needed to swim. Thanks to our exhaustive simulations we were able to elucidate the effect of light on the growth of D. shibae, to study the consequences of genetic perturbations, and to identify mutants which produce more cloud-seeding compounds. Foremost, our computational results help to understand an important part of the complex processes in the ocean in greater detail. Besides, they can be a valuable guide for future wet-lab experiments.

Bacillus megaterium has both a functional BluB protein required for DMB synthesis and a related flavoprotein that forms a stable radical species

Despite the extensive study of the biosynthesis of the complex molecule B12 (cobalamin), the mechanism by which the lower ligand 5,6-dimethylbenzimidazole (DMB) is formed has remained something of a mystery. However, recent work has identified and characterized a DMB-synthase (BluB) responsible for the oxygen-dependent, single enzyme conversion of FMN to DMB. In this work, we have identified BluB homologs from the aerobic purple, nonsulfur, photosynthetic bacterium Rhodobacter capsulatus and the aerobic soil bacterium Bacillus megaterium and have demonstrated DMB synthesis by the use of a novel complementation assay in which a B12 deficient strain, substituted with the precursor cobinamide is recovered either by the addition of DMB or by the recombinant expression of a bluB gene. The DMB-synthetic activity of the purified recombinant BluB enzymes was further confirmed in vitro by providing the enzyme with FMNH2 and oxygen and observing the formation of DMB by HPLC. The formation of a 4a-peroxyflavin intermediate, the first step in the oxygen dependent mechanism of DMB biosynthesis, is reported here and is the first intermediate in the enzyme catalysed reaction to be demonstrated experimentally to date. The identification and characterization of an FMN-binding protein found on the cobI operon of B. megaterium, CbiY, is also detailed, revealing an FMN-containing enzyme which is able to stabilize a blue flavin semiquinone upon reduction with a 1-electron donor.

Active site residues critical for flavin binding and 5,6-dimethylbenzimidazole biosynthesis in the flavin destructase enzyme BluB

The "flavin destructase" enzyme BluB catalyzes the unprecedented conversion of flavin mononucleotide (FMN) to 5,6-dimethylbenzimidazole (DMB), a component of vitamin B(12). Because of its unusual chemistry, the mechanism of this transformation has remained elusive. This study reports the identification of 12 mutant forms of BluB that have severely reduced catalytic function, though most retain the ability to bind flavin. The "flavin destructase" BluB is an unusual enzyme that fragments the flavin cofactor FMNH(2) in the presence of oxygen to produce 5,6-dimethylbenzimidazole (DMB), the lower axial ligand of vitamin B(12) (cobalamin). Despite the similarities in sequence and structure between BluB and the nitroreductase and flavin oxidoreductase enzyme families, BluB is the only enzyme known to fragment a flavin isoalloxazine ring. To explore the catalytic residues involved in this unusual reaction, mutants of BluB impaired in DMB biosynthesis were identified in a genetic screen in the bacterium Sinorhizobium meliloti. Of the 16 unique point mutations identified in the screen, the majority were located in conserved residues in the active site or in the unique "lid" domain proposed to shield the active site from solvent. Steady-state enzyme assays of 12 purified mutant proteins showed a significant reduction in DMB synthesis in all of the mutants, with eight completely defective in DMB production. Ten of these mutants have weaker binding affinities for both oxidized and reduced FMN, though only two have a significant effect on complex stability. These results implicate several conserved residues in BluB's unique ability to fragment FMNH(2) and demonstrate the sensitivity of BluB's active site to structural perturbations. This work lays the foundation for mechanistic studies of this enzyme and further advances our understanding of the structure-function relationship of BluB.