Expression and characterization of catechol 1,2-dioxygenase from Oceanimonas marisflavi 102-Na3

Bioremediation of naphthenic acid by Bacillus subtilis: Degradation kinetics and pathway elucidation

Naphthenic acids, toxic and persistent carboxylic acids found in petroleum contaminated water, pose a significant environmental challenge, but bioremediation offers a promising and cost-effective solution for their treatment. The present study illustrates the ability of Bacillus subtilis to degrade commercial naphthenic acid (100 mg/L) in aerobic and microaerobic settings under optimized conditions (temperature 36 °C, pH 6.0, and salinity 0.5 %). The degradation was confirmed by 47.61 ± 3.609 % reduction in total organic carbon levels within 144 h, indicating the microbial potential to mineralize organic naphthenic acid in aqueous medium as a sole carbon source. Naphthenic acids, being structurally complex and comprising a diverse array of carboxylic acids, were further studied using two representative models, hexanoic acid (linear) and benzoic acid (aromatic). These representative acids were selected to investigate the degradation kinetics and to elucidate the underlying degradation mechanism. The growth kinetics of B. subtilis on hexanoic acid and benzoic acid followed the Monod growth model, with maximum specific growth rates (μmax) of 0.17344 ± 0.004 and 0.15088 ± 0.006 day-1 respectively. The biodegradation kinetics followed a non-linear first-order rate model, with rate constants (k) of 0.43 ± 0.084 h-1 for hexanoic acid and 0.12 ± 0.02 h-1 for benzoic acid. Corresponding half-lives (t1/2) were determined as 13.37 h for hexanoic acid and 29.52 h for benzoic acid, demonstrating a faster degradation rate for hexanoic acid compared to benzoic acid. GC-MS analysis elucidated the degradation pathway, catechol and muconic acid were identified as the key intermediates, which suggest a potential metabolic breakdown. Consequently, it demonstrates the potential of Bacillus subtilis for the effective removal of naphthenic acids from polluted wastewater.

Harnessing nature's catalysts: Advances in enzymatic alkene cleavage

Double bonds are prevalent in various substrates and renewable feedstocks, and their cleavage typically necessitates harsh reaction conditions involving high temperatures, organic solvents, and hazardous catalysts such as heavy metals or ozone. This review explores the sustainable enzymatic alternatives developed by nature for alkene cleavage. It provides a comprehensive overview of alkene-cleaving enzymes, detailing their mechanisms, substrate specificities, and applications. The enzymes discussed include those acting on aliphatic, cyclic, and activated aromatic systems. Emphasizing the significance of these biocatalysts in green chemistry and biocatalysis, this review highlights their potential to replace traditional chemical oxidants with safer, cost-effective, and environmentally friendly options. Future research directions include expanding enzyme substrate scopes, enhancing their operational stability and activity, and integrating them into scalable processes for broader application in the pharmaceutical, flavor, and fragrance industries.

Oceanimonas pelagia sp. nov., a novel biosurfactant-producing and plastic-degrading potential bacterium isolated from marine coastal sediment

A marine bacterial strain, named NTOU-MSR1T, was isolated from marine sediment of northern coast of Taiwan. This bacterium was Gram-stain-negative, aerobic, and motile, with a single flagellum. Its rod-shaped cells measured approximately 0.5-0.6 µm in width and 1.8-2.0 μm in length. NTOU-MSR1T grew at temperatures ranging from 10 to 45 °C, optimally at 30 °C. The pH range for growth was 7.0-10.0, with optimal growth at pH 7.0-8.0. It tolerated NaCl concentrations up to 12%. The cell membrane predominantly contained fatty acids such C16:1ω7c, C18:1ω7c, and C16:0. The overall genome relatedness indices indicated that strain NTOU-MSR1T had an average nucleotide identity (ANI) of 87.88% and a digital DNA-DNA hybridization (dDDH) value of 35.40% compared to its closest related species, O. marisflavi 102-Na3T. These values fell below the 95% and 70% threshold for species delineation, respectively. These findings suggested that the strain NTOU-MSR1T was a new member of the Oceanimonas genus. Its genomic DNA had a G + C content of 61.0 mol%. Genomic analysis revealed genes associated with the catechol branch of β- ketoadipate pathway for degrading polycyclic aromatic hydrocarbons, resistance to heavy metal, biosynthesis of polyhydroxybutyrate and the production of glycoside hydrolases (GH19, GH23, and GH103) for chitin and glycan digestion. Additionally, NTOU-MSR1T was capable of synthesizing biosurfactants and potentially degrading plastic. The proposed name for this new species is Oceanimonas pelagia, with the type strain designated as NTOU-MSR1T (= BCRC 81403T = JCM 36023T).

Identification and characterization of a novel high-activity amylosucrase from Salinispirillum sp. LH10-3-1

In this study, a novel high-activity amylosucrase from Salinispirillum sp. LH10-3-1 (SaAS) was identified and characterized. The recombinant enzyme was determined as a monomer with a molecular mass of 75 kDa. SaAS protein exhibited the maximum total and polymerization activities at pH 9.0 and maximum hydrolysis activity at pH 8.0. The optimum temperature for total, polymerization, and hydrolysis activities were 40, 40, and 45 °C, respectively. Under the optimal pH and temperature, SaAS had a specific activity of 108.2 U/mg. SaAS also showed excellent salt tolerance and could retain 77.4% of its original total activity at 4.0 M NaCl. The addition of Mg²⁺, Ba²⁺, and Ca²⁺ enhanced the total activity of SaAS. When the conversion of 0.1 M and 1.0 M sucrose was catalyzed at pH 9.0 and 40 °C for 24 h, the ratios of hydrolysis, polymerization, and isomerization reactions were 11.9:77.4:10.7 and 15.3:53.5:31.2, respectively. The α-arbutin yield of 60.3% was achieved from 20 mM sucrose and 5 mM hydroquinone catalyzed by SaAS. KEY POINTS: • A novel amylosucrase from Salinispirillum sp. LH10-3-1 (SaAS) was characterized. • SaAS has the highest specific enzyme activity among all known amylosucrase. • SaAS has hydrolysis, polymerization, isomerization, and glucosyltransferase activities.

Insights into the Binding Interaction of Catechol 1,2-Dioxygenase with Catechol in Achromobacter xylosoxidans DN002

Microbial remediation has become one of the promising ways to eliminate polycyclic aromatic hydrocarbons (PAHs) pollution due to its efficient enzyme metabolism system. Catechol 1,2-dioxygenase (C12O) is a crucial rate-limiting enzyme in the degradation pathway of PAHs in Achromobacter xylosoxidans DN002 that opens the benzene ring through the ortho-cleavage pathway. However, little attention has been given to explore the interaction mechanism of relevant enzyme-substrate. This study aims to investigate the binding interaction between C12O of strain DN002 and catechol by means of a molecular biological approach combined with homology modeling, molecular docking, and multiple spectroscopies. The removal rate of catechol in the mutant strain of cat A deletion was only 12.03%, compared to the wild-type strain (54.21%). A Ramachandran plot of active site regions of the primary amino acid sequences in the native enzyme showed that 93.5% sequences were in the most favored regions on account of the results of homology modeling, while an additional 6.2% amino acid sequences were found in conditionally allowed regions, and 0.4% in generously allowed regions. The binding pocket of C12O with catechol was analyzed to obtain that the catalytic trimeric group of Tyr164-His224-His226 was proven to be great vital for the ring-opening reaction of catechol by molecular docking. In the native enzyme, binding complexes were spontaneously formed by hydrophobic interactions. Binding constants and thermodynamic potentials from fluorescence spectra indicated that catechol effectively quenched the intrinsic fluorescence of C12O in the C12O/catechol complex via conventional static and dynamic quenching mechanisms of C12O. The results of ultraviolet and visible (UV) spectra, synchronous fluorescence, and circular dichroism (CD) spectra revealed conspicuous changes in the local conformation, and site-directed mutagenesis confirmed the role of predicted key residues during catalysis, wherein His₂₂₆ had a significant effect on catechol utilization by C12O. This is the first report to reveal interactions of C12O with substrate from the molecular docking results, providing the mechanistic understanding of representative dioxygenases involved in aromatic compound degradation, and a solid foundation for further site modifications as well as strategies for the directed evolution of this enzyme.

Genome analysis of a plastisphere-associated Oceanimonas sp. NSJ1 sequenced on Nanopore MinION platform

Oceanimonas sp. NSJ1 was isolated from macroplastic debris collected previously from Junput, an intertidal beach, facing the northeast coastal Bay of Bengal of the Northern Indian Ocean. The genome of this isolate is closely related to Oceanimonas doudoroffii with a genome size of 3.56 Mbp. The genome annotation confirmed the presence of 5919 total genes, out of which 5809 were CDSs (coding sequences) and all are protein-coding. The genome codes for 110 RNA with 25 rRNA, 84 tRNA (transfer RNA), and one tmRNA (transfer-messenger RNA). Analyses of the annotated genome of Oceanimonas sp. NSJ1 revealed the presence of enzymes involved in the degradation of polycyclic aromatic hydrocarbons. The presence of phthalate 4,5-dioxygenase oxygenase reductase subunit pht2 within the genome also highlights the novelty of this isolate and future functional potential for studying phthalate degradation in marine environment.