Protocatechuate 3,4-dioxygenase: a wide substrate specificity enzyme isolated from Stenotrophomonas maltophilia KB2 as a useful tool in aromatic acid biodegradation

Degradation of 2,4,6-Trinitrotoluene (TNT): Involvement of Protocatechuate 3,4-Dioxygenase (P34O) in Buttiauxella sp. S19-1

Extensive use and disposal of 2,4,6-trinitrotoluene (TNT), a primary constituent of explosives, pollutes the environment and causes severe damage to human health. Complete mineralization of TNT via bacterial degradation has recently gained research interest as an effective method for the restoration of contaminated sites. Here, screening for TNT degradation by six selected bacteria revealed that Buttiauxella sp. S19-1, possesses the strongest degrading ability. Moreover, BuP34O (a gene encoding for protocatechuate 3,4-dioxygenase—P34O, a key enzyme in the β-ketoadipate pathway) was upregulated during TNT degradation. A knockout of BuP34O in S19-1 to generate S-M1 mutant strain caused a marked reduction in TNT degradation efficiency compared to S19-1. Additionally, the EM1 mutant strain (Escherichia coli DH5α transfected with BuP34O) showed higher degradation efficiency than DH5α. Gas chromatography mass spectrometry (GC-MS) analysis of TNT degradation by S19-1 revealed 4-amino-2,6-dinitrotolune (ADNT) as the intermediate metabolite of TNT. Furthermore, the recombinant protein P34O (rP34O) expressed the activity of 2.46 µmol/min·mg. Our findings present the first report on the involvement of P34O in bacterial degradation of TNT and its metabolites, suggesting that P34O could catalyze downstream reactions in the TNT degradation pathway. In addition, the TNT-degrading ability of S19-1, a Gram-negative marine-derived bacterium, presents enormous potential for restoration of TNT-contaminated seas.

Role of Water Hydrogen Bonding on Transport of Small Molecules inside Hydrophobic Channels

We conducted a systematic analysis of water networking inside smooth hyperboloid hydrophobic structures (cylindrical, barrel, and hourglass shapes) to elucidate the role of water hydrogen bonding on the transport of small hydrophobic molecules (ligands). Through a series of molecular dynamics simulations, we established that a hydrogen-bonded network forming along the centerline resulted in a water exclusion zone adjacent to the walls. The size of the exclusion zone is a function of the geometry and the nonbonded interaction strength, defining the effective hydrophobicity of the structure. Exclusion of water molecules from this zone results in lower apparent viscosity, leading to acceleration of ligand transport up to 7 times faster than that measured in the bulk. Transport of ligands into and out of the hydrophobic structures was shown to be controlled by a single water molecule that capped the narrow regions in the structure. This mechanism provides physical insights into the behavior and role of water in the bottleneck regions of hydrophobic enzyme channels. These findings were then used in a sister publication [ Escalante , D. E. , Comput. Struct. Biotechnol. J. 2019 17 757 760 ] to develop a model that can accurately predict the transport of ligands along nanochannels of broad-substrate specificity enzymes.

Naproxen ecotoxicity and biodegradation by Bacillus thuringiensis B1(2015b) strain

High level of naproxen consumption leads to the appearance of this drug in the environment but its possible effects on non-target organisms together with its biodegradation are not well studied. The aim of this work was to evaluate naproxen ecotoxicity by using the Microbial Assay for Risk Assessment. Moreover, Bacillus thuringiensis B1(2015b) was tested for both ecotoxicity and the ability of this strain to degrade naproxen in cometabolic conditions. The results indicate that the mean value of microbial toxic concentration estimated by MARA test amounts to 1.66 g/L whereas EC₅₀ of naproxen for B1(2015b) strain was 4.69 g/L. At toxic concentration, Bacillus thuringiensis B1(2015b) showed 16:0 iso 3OH fatty acid presence and an increase in the ratio of total saturated to unsaturated fatty acids. High resistance of the examined strain to naproxen correlated with its ability to degrade this drug in cometabolic conditions. The results of bacterial reverse mutation assay (Ames test) revealed that naproxen at concentrations above 1 g/L showed genotoxic effect but the response was not dose-dependent. Maximal specific naproxen removal rate was observed at pH 6.5 and 30 °C, and in the presence of 0.5 g/L glucose as a growth substrate. Kinetic analysis allowed estimation of the half saturation constant (K_s) and the maximum specific naproxen removal rate (q_max) as 6.86 mg/L and 1.26 mg/L day, respectively. These results indicate that Bacillus thuringiensis B1(2015b) has a high ability to degrade naproxen and is a potential tool for bioremediation.

Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity

Delftia tsuruhatensis MTQ3 is a plant growth-promoting rhizobacterium (PGPR) isolated from tobacco rhizosphere. Here, we report the draft genome sequence of D. tsuruhatensis MTQ3. Several functional genes related to antimicrobial activity and environment adaption have been found in the genome. This is the first genome sequence of D. tsuruhatensis related to PGPR.

Selective requirement of the shikimate pathway of Legionella pneumophila for intravacuolar growth within human macrophages but not within Acanthamoeba

Legionella pneumophila utilizes the Dot/Icm type IV translocation system to proliferate within a vacuole in a wide variety of natural amoebal hosts and in alveolar macrophages of the human accidental host. Although L. pneumophila utilizes host amino acids as the main sources of carbon and energy, it is not known whether de novo synthesis of amino acids by intravacuolar L. pneumophila contributes to its nutrition. The aroB and aroE genes encode enzymes for the shikimate pathway that generates the aromatic amino acids Phe, Trp, and Tyr. Here we show the aroB and aroE mutants of L. pneumophila to be defective in growth in human monocyte-derived macrophages (hMDMs) but not in Acanthamoeba spp. The aroB and aroE mutants are severely attenuated in intrapulmonary proliferation in the A/J mouse model of Legionnaires' disease, and the defect is fully complemented by the respective wild-type alleles. The two mutants grow normally in rich media but do not grow in defined media lacking aromatic amino acids, and the growth defect is rescued by inclusion of the aromatic amino acids, which are essential for production of the pyomelanin pigment. Interestingly, supplementation of infected hMDMs with the three aromatic amino acids or with Trp alone rescues the intramacrophage defect of the aroE but not the aroB mutant. Therefore, the shikimate pathway of L. pneumophila is differentially required for optimal growth within human macrophages, which are auxotrophic for Trp and Phe, but is dispensable for growth within the Acanthamoeba spp. that synthesize the aromatic amino acids.