A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants

Regulate catalytic performance by engineering non-regular structure of extradiol dioxygenase: An entrance to bottom strategy

Extradiol dioxygenase Tcu3516 is a home-sourced enzyme demonstrating potent aromatic phenol degradation capacity. To add to the advantageous modifications inside active cavity, this work reported a novel strategy to engineer rarely concerned non-regular structures around the entrance towards the active site at the bottom of cavity. Three structures, Loop region 1 (Loop1: Met173-Arg185), Loop region 2 (Loop2: Ala201-Val212) and C-terminal (C-tail: His290-Lys306) were therefore identified through structural flexibility analysis. Highly rigid prolines within the structures were mutated into smaller alanine, glycine, or serine to improve structural flexibilities; while only P183S on Loop1 showed 3-fold activity enhancement vs the WT when subjected to cleavage of mono-cyclic catechol analogues. The analysis of Root Mean Square Fluctuation showed that P183S presents certain enhancement on Loop1 flexibility without dramatic changes of other domains. Furthermore, the synergetic effects from mutation P183S and cavity-based mutations V186L, V212N and D285A were evaluated by characterizing combinatorial mutants. Temperature dependence and thermostability of the combined mutants showed a more flexible catalytic domain without sacrificing structural integrity and stability. kcat value of P183S/V186L (SL) towards monocyclic catechols significantly surpasses any other combinatorial mutants around Tcu3516 active sites. Moreover, the synergetic effects on conformational plasticity were analyzed by molecular dynamic simulations to shed light into the interplay between structural changes and catalytic performance.

Fenton-ultrasound treatment of corn stalks enhances humification during composting by stimulating the inheritance and synthesis of polyphenolic compounds-preliminary evidence from a laboratory trial

The impact of Fenton-ultrasound treatment on the production of polyphenols and humic acid (HA) during corn stalk composting was investigated by analyzing the potential for microbial assimilation of polysaccharides in corn stalks to generate polyphenols using a13C-glucose tracer. The results showed that Fenton-ultrasound treatment promoted the decomposition of lignocellulose and increased the HA content, degree of polymerization (DP), and humification index (HI). The primary factor could be attributed to Fenton-ultrasound treatment-induced enhanced the abundance of lignocellulose-degrading microorganisms, as Firmicutes, Actinobacteria phylum and Aspergillis genus, which serve as the primary driving forces behind polyphenol and HA formation. Additionally, the utilization of a13C isotope tracer revealed that corn stalk polysaccharide decomposition products can be assimilated by microbes and subsequently secrete polyphenolic compounds. This study highlights the potential of microbial activity to generate phenolic compounds, offering a theoretical basis for increasing polyphenol production and promoting HA formation during composting.

Competitive mechanism of salt-tolerance/degradation-performance of organic pollutant in bacteria: Na+/H+ antiporters contribute to salt-stress resistance but impact phenol degradation

Phenolic-laden wastewater is typically characterized by its high toxicity and high salinity, imposing serious limits on the application of bioremediation. Although a few halotolerant microorganisms have been reported to degrade phenol, their removal efficiency on high concentrations of phenol remains unsatisfactory. What's more, the deep interaction molecular mechanism of salt-tolerance/phenol-degradation performance has not been clearly revealed. Here, a halotolerant strain Aeribacillus pallidus W-12 employed a meta-pathway to efficiently degrade high concentration of phenol even under high salinity conditions. Investigation of salt-tolerance strategy indicated that four Na+/H+ antiporters, which are widely distributed in bacteria, synergistically endowed the strain with excellent salt adaptability. All these antiporters differentially but positively responded to salinity changes and induction of phenol, forming a synergistic transport effect on salt ions and phenol. In-depth analysis revealed a competitive relationship between salt tolerance and degradation performance, which significantly impaired the degradation efficiency at relatively high salinity. The efficient degradation performance of W-12 under different phenol concentrations and salinity conditions indicated its bioremediation potential for multiple types of phenolic wastewater. Collectively, the competitive mechanism of salt tolerance and degradation performance enlightens a new strategy of introducing or re-constructing Na+/H+ antiporters to further improve bioremediation efficiency of hypersaline organic wastewater.

Engineering non-conservative substrate recognition sites of extradiol dioxygenase: Computation guided design to diversify and accelerate degradation of aromatic compounds

Extradiol dioxygenases (EDOs) catalyzing meta-cleavage of catecholic compounds promise an effective way to detoxify aromatic pollutants. This work reported a novel scenario to engineer our recently identified Type I EDO from Tcu3516 for a broader substrate scope and enhanced activity, which was based on 2,3-dihydroxybiphenyl (2,3-DHB)-liganded molecular docking of Tcu3516 and multiple sequence alignment with other 22 Type I EDOs. 11 non-conservative residues of Tcu3516 within 6 Å distance to the 2,3-DHB ligand center were selected as potential hotspots and subjected to semi-rational design using 6 catecholic analogues as substrates; the mutants V186L and V212N returned with progressive evolution in substrate scope and catalytic activity. Both mutants were combined with D285A for construction of double mutants and final triple mutant V186L/V212N/D285A. Except for 2,3-DHB (the mutant V186L/D285A gave the best catalytic performance), the triple mutant prevailed all other 5 catecholic compounds for their degradation; affording the catalytic efficiency kcat/Km value increase by 10-30 folds, protein Tm (structural rigidity) increase by 15 °C and the half-life time enhancement by 10 times compared to the wild type Tcu3516. The molecular dynamic simulation suggested that a stabler core and a more flexible entrance are likely accounting for enhanced catalytic activity and stability of enzymes.

Efficient bio-remediation of multiple aromatic hydrocarbons using different types of thermotolerant, ring-cleaving dioxygenases derived from Aeribacillus pallidus HB-1

As toxic contaminants, aromatic compounds are widespread in most environmental matrices, and bioenzymatic catalysis plays a critical role in the degradation of xenobiotics. Here, a thermophillic aromatic hydrocarbon degrader Aeribacillus pallidus HB-1 was found. Bioinformatic analysis of the HB-1 genome revealed two ring-cleaving extradiol dioxygenases (EDOs), among which, EDO-0418 was assigned to a new subfamily of type I.1 EDOs and exhibited a broad substrate specificity, particularly towards biarylic substrate. Both EDOs exhibited optimal activities at elevated temperatures (55 and 65 °C, respectively) and showed remarkable thermostability, pH stability, metal ion resistance and tolerance to chemical reagents. Most importantly, simulated wastewater bioreactor experiments demonstrated efficient and uniform degradation performance of mixed aromatic substrates under harsh environments by the two enzymes combined for potential industrial applications. The unveiling of two thermostable dioxygenases with broad substrate specificities and stress tolerance provides a novel approach for highly efficient environmental bioremediation using composite enzyme systems.

Electrophoretic characterization of cellular and extracellular proteins from Selenastrum capricornutum cultures degrading benzo(a)pyrene and their identification by UPLC-ESI-TOF mass spectrometry

Selenastrum capricornutum efficiently degrades benzo(a)pyrene (BaP) but few proteins related to BaP degradation have been identified in this microalgae. So far, it has only been suggested that it could degrade BaP via the monooxygenase and/or dioxygenase pathways. To know more about this fact, in this work, cultures of S. capricornutum incubated with BaP were used to obtain the molecular weights (MWs) of proteins existing in its extra- and cellular extracts by electrophoresis and UPLC-ESI(+)-TOF MS analysis. The results of this proteomic approach indicated that BaP markedly induces the MWs: 6-20, 30, 45, and 65 kDa in cells; 6-20, 30.3, 38-45, and 55 kDa in liquid medium. So, these proteins could be related to BaP biodegradation. An identified protein with monooxygenase activity and rubredoxins (Rds) show to be related to BaP degradation: Rds could participate, together with the monooxygenase in the electron transfer during the formation of monohydroxylated-BaP metabolites. Rds may be also associated with a dioxygenase system that degrades BaP to form dihydrodiol-BaP metabolites. A multi-pass membrane protein was identified too, and it can regulate the transport of molecules like enzymes from inside the cell to the outside environment. At the same time, the presence of a dihydrolipoamide acetyltransferase validated the stress caused by the exposure to BaP. It is noteworthy that these findings provide valuable and original information on the characterization of the proteins of S. capricornutum cultures degrading BaP, whose enzymes have so far not been known. It is important to highlight that the functions of the identified proteins can help in understanding the metabolic and environmental behavior of this microalgae, and the extracts containing the degrading enzymes could be utilized in bioremediation applications.

The capability of chloramphenicol biotransformation of Klebsiella sp. YB1 under cadmium stress and its genome analysis

Co-contamination by antibiotics and heavy metal is common in the environment, however, there is scarce information about antibiotics biodegradation under heavy metals stress. In this study, Klebsiella sp. Strain YB1 was isolated which is capable of biodegrading chloramphenicol (CAP) with a biodegradation efficiency of 22.41% at an initial CAP of 10 mg L^-1 within 2 days. CAP biodegradation which fitted well with the first-order kinetics. YB1 still degrades CAP under Cd stress, however 10 mg L^-1 Cd inhibited CAP biodegradation by 15.1%. Biotransformation pathways remained the same under Cd stress, but two new products (Cmpd 19 and Cmpd 20) were identified. Five parallel metabolism pathways of CAP were proposed with/without Cd stress, including one novel pathway (pathway 5) that has not been reported before. In pathway 5, the initial reaction was oxidation of CAP by disruption of C-C bond at the side chain of C1 and C2 with the formation of 4-nitrobenzyl alcohol and CY7, then these intermediates were oxidized into p-nitrobenzoic acid and CY1, respectively. CAP acetyltransferase and nitroreductase and 2,3/4,5-dioxygenase may play an important role in CAP biodegradation through genome analysis and prediction. This study deepens our understanding of mechanism of antibiotic degradation under heavy metal stress in the environment.

A novel Bacillus ligniniphilus catechol 2,3-dioxygenase shows unique substrate preference and metal requirement

Identification of novel enzymes from lignin degrading microorganisms will help to develop biotechnologies for biomass valorization and aromatic hydrocarbons degradation. Bacillus ligniniphilus L1 grows with alkaline lignin as the single carbon source and is a great candidate for ligninolytic enzyme identification. The first dioxygenase from strain L1 was heterologously expressed, purified, and characterized with an optimal temperature and pH of 32.5 °C and 7.4, respectively. It showed the highest activity with 3-ethylcatechol and significant activities with other substrates in the decreasing order of 3-ethylcatechol > 3-methylcatechol > 3-isopropyl catechol > 2, 3-dihydroxybiphenyl > 4-methylcatechol > catechol. It did not show activities against other tested substrates with similar structures. Most reported catechol 2,3-dioxygenases (C23Os) are Fe²⁺-dependent whereas Bacillus ligniniphilus catechol 2,3-dioxygenase (BLC23O) is more Mn²⁺- dependent. At 1 mM, Mn²⁺ led to 230-fold activity increase and Fe²⁺ led to 22-fold increase. Sequence comparison and phylogenetic analyses suggested that BL23O is different from other Mn-dependent enzymes and uniquely grouped with an uncharacterized vicinal oxygen chelate (VOC) family protein from Paenibacillus apiaries. Gel filtration analysis showed that BLC23O is a monomer under native condition. This is the first report of a C23O from Bacillus ligniniphilus L1 with unique substrate preference, metal-dependency, and monomeric structure.