Bacterial pyridine hydroxylation is ubiquitous in environment

Genomic and transcriptomic analyses provide new insights into the allelochemical degradation preference of a novel Acinetobacter strain

A novel n-alkane- and phenolic acid-degrading Acinetobacter strain (designated C16S1T) was isolated from rhizosphere soil. The strain was identified as a novel species named Acinetobacter suaedae sp. nov. using a polyphasic taxonomic approach. Strain C16S1T showed preferential degradation of three compounds: p-hydroxybenzoate (PHBA) > ferulic acid (FA) > n-hexadecane. In a medium containing two or three of these allelochemicals, coexisting n-hexadecane and PHBA accelerated each other's degradation and that of FA. FA typically hindered the degradation of n-hexadecane but accelerated PHBA degradation. The upregulated expression of n-hexadecane- and PHBA-degrading genes induced, by their related substrates, was mutually enhanced by coexisting PHBA or n-hexadecane; in contrast, expression of both gene types was reduced by FA. Coexisting PHBA or n-hexadecane enhanced the upregulation of FA-degrading genes induced by FA. The expressions of degrading genes affected by coexisting chemicals coincided with the observed degradation efficiencies. Iron shortage limited the degradation efficiency of all three compounds and changed the degradation preference of Acinetobacter. The present study demonstrated that the biodegradability of the chemicals, the effects of coexisting chemicals on the expression of degrading genes and the strain's growth, the shortage of essential elements, and the toxicity of the chemicals were the four major factors affecting the removal rates of the coexisting allelochemicals.

Structural characteristics and microbial function of biofilm in membrane-aerated biofilm reactor for the biodegradation of volatile pyridine

In order to avoid the serious air pollution caused by the volatilization of high recalcitrant pyridine, membrane-aerated biofilm reactor (MABR) with bubble-free aeration was used in this study, with the structural characteristics and microbial function of biofilm emphasized. The results showed that as high as 0.6 kg·m^-3·d^-1 pyridine could be completely removed in MABR. High pyridine loading thickened the biofilm, but without obvious detachment observed. The distinct stratification of microbes and extracellular polymeric substances were shaped by elevated pyridine load, enhancing the structural heterogeneity of biofilm. The increased tryptophan-like substances as well as α-helix and β-sheet proportion in proteins stabilized the biofilm structure against high influent loading. Based on the identified intermediates, possible pyridine biodegradation pathways were proposed. Multi-omics analyses revealed that the metabolic pathways with initial hydroxylation and reduction reaction was enhanced at high pyridine loading. The functional genes were mainly associated with Pseudomonas and Delftia, might responsible for pyridine biodegradation. The results shed light on the effective treatment of wastewater containing recalcitrant pollutants such as pyridine via MABR.

An efficient and regioselective biocatalytic synthesis of aromatic N-oxides by using a soluble di-iron monooxygenase PmlABCDEF produced in the Pseudomonas species

Here, we present an improved whole-cell biocatalysis system for the synthesis of heteroaromatic N-oxides based on the production of a soluble di-iron monooxygenase PmlABCDEF in Pseudomonas sp. MIL9 and Pseudomonas putida KT2440. The presented biocatalysis system performs under environmentally benign conditions, features a straightforward and inexpensive procedure and possesses a high substrate conversion and product yield. The capacity of gram-scale production was reached in the simple shake-flask cultivation. The template substrates (pyridine, pyrazine, 2-aminopyrimidine) have been converted into pyridine-1-oxide, pyrazine-1-oxide and 2-aminopyrimidine-1-oxide in product titres of 18.0, 19.1 and 18.3 g l-1 , respectively. To our knowledge, this is the highest reported productivity of aromatic N-oxides using biocatalysis methods. Moreover, comparing to the chemical method of aromatic N-oxides synthesis based on meta-chloroperoxybenzoic acid, the developed approach is applicable for a regioselective oxidation that is an additional advantageous option in the preparation of the anticipated N-oxides.

Evaluating the effect of fenton pretreated pyridine wastewater under different biological conditions: Microbial diversity and biotransformation pathways

Pyridine contamination poses a significant threat to human and environmental health. Due to the presence of nitrogen atom in the pyridine ring, the pi bond electrons are attracted toward it and make difficult for pyridine treatment with biological and chemical methods. In this study, coupling Fenton treatment with different biological process was designed to enhance pyridine biotransformation and further mineralization. After Fenton oxidation process optimized, pretreated pyridine was evaluated under three biological (anaerobic, aerobic and microaerobic) operating conditions. Under optimum Fenton oxidation, pyridine (30-75%) and TOC (5-25%) removal efficiencies were poor. Biological process alone also showed insignificant removal efficiency, particularly anaerobic (pyridine = 8.2%; TOC = 5.3%) culturing condition. However, combining Fenton pretreatment with biological process increased pyridine (93-99%) and TOC (87-93%) removals, suggesting that hydroxyl radical generated during Fenton oxidation enhanced pyridine hydroxylation and further mineralization in the biological (aerobic > microaerobic > anaerobic) process. Intermediates were analyzed with UPLC-MS and showed presence of maleic acid, pyruvic acid, glutaric dialdehyde, succinic semialdehyde and 4-formylamino-butyric acid. High-throughput sequencing analysis also indicated that Proteobacteria (35-43%) followed by Chloroflexi (10.6-24.3%) and Acidobacteria (8.0-29%) were the dominant phyla detected in the three biological treatment conditions. Co-existence of dominant genera under aerobic/microaerobic (Nitrospira > Dokdonella > Caldilinea) and anaerobic (Nitrospira > Caldilinea > Longilinea) systems most probably play significant role in biotransformation of pyridine and its intermediate products. Overall, integrating Fenton pretreatment with different biological process is a promising technology for pyridine treatment, especially the combined system enhanced anaerobic (>10 times) microbial pyridine biotransformation activity.

Insights into electroactive biofilms for enhanced phenolic degradation of coal pyrolysis wastewater (CPW) by magnetic activated coke (MAC): Metagenomic analysis in attached biofilm and suspended sludge

To investigate the role of electroactive biofilms for enhanced phenolic degradation, lignite activated coke (LAC) and MAC were used as carriers in moving-bed biofilm reactor (MBBR) for CPW treatment. In contrast to activated sludge (AS) reactor, the carriers improved degradation performance of MBBR. Although two MBBRs exerted similar degradation capacity with over 92% of COD and 93% phenols removal under the highest phenolics concentration (500 mg/L), the effluent of MAC-based MBBR remained higher biodegradability (BOD₅/COD = 0.34 vs 0.18) than that of LAC-based MBBR. Metagenomic analysis revealed that electroactive biofilms determined phenolic degradation of MAC-based MBBR. Primarily, Geobacter (17.33%) started Fe redox cycle on biofilms and developed syntrophy with Syntrophorhabdus (6.47%), which fermented phenols into easily biodegradable substrates. Subsequently, Ignavibacterium (3.38% to 2.52%) and Acidovorax (0.46% to 8.83%) conducted biological electricity from electroactive biofilms to suspended sludge. They synergized with dominated genus in suspended sludge, Alicycliphilus (19.56%) that accounted for phenolic oxidation and nitrate reduction. Consequently, the significantly advantage of Geobater and Syntrophorhabdus was the keystone reason for superior biodegradability maintenance of MAC-based MBBR.

Microbial Degradation of Pyridine: a Complete Pathway in Arthrobacter sp. Strain 68b Deciphered

Pyridine and its derivatives constitute the majority of heterocyclic aromatic compounds that occur largely as a result of human activities and contribute to environmental pollution. It is known that they can be degraded by various bacteria in the environment; however, the degradation of unsubstituted pyridine has not yet been completely resolved. In this study, we present data on the pyridine catabolic pathway in Arthrobacter sp. strain 68b at the level of genes, enzymes, and metabolites. The pyr gene cluster, responsible for the degradation of pyridine, was identified in a catabolic plasmid, p2MP. The pathway of pyridine metabolism consisted of four enzymatic steps and ended by the formation of succinic acid. The first step in the degradation of pyridine proceeds through a direct ring cleavage catalyzed by a two-component flavin-dependent monooxygenase system, encoded by pyrA (pyridine monooxygenase) and pyrE genes. The genes pyrB, pyrC, and pyrD were found to encode (Z)-N-(4-oxobut-1-enyl)formamide dehydrogenase, amidohydrolase, and succinate semialdehyde dehydrogenase, respectively. These enzymes participate in the subsequent steps of pyridine degradation. The metabolites of these enzymatic reactions were identified, and this allowed us to reconstruct the entire pyridine catabolism pathway in Arthrobacter sp. 68b.IMPORTANCE The biodegradation pathway of pyridine, a notorious toxicant, is relatively unexplored, as no genetic data related to this process have ever been presented. In this paper, we describe the plasmid-borne pyr gene cluster, which includes the complete set of genes responsible for the degradation of pyridine. A key enzyme, the monooxygenase PyrA, which is responsible for the first step of the catabolic pathway, performs an oxidative cleavage of the pyridine ring without typical activation steps such as reduction or hydroxylation of the heterocycle. This work provides new insights into the metabolism of N-heterocyclic compounds in nature.

In vitro reconstitution of the biosynthetic pathway of 3-hydroxypicolinic acid

3-Hydroxypicolinic acid (3-HPA) is an important pyridine building block of bacterial secondary metabolites. Although the main biosynthetic pathways of these metabolites have been identified and well characterized, the enzymatic mechanism underlying the biosynthesis of 3-HPA has yet to be elucidated. In this work, we successfully reconstituted the complete biosynthetic pathway of 3-HPA in vitro. We showed that an l-lysine 2-aminotransferase, a two-component monooxygenase, and a FAD-dependent dehydrogenase are required to convert l-lysine to 3-HPA. We further demonstrated that 3-HPA does not derive from the direct hydroxylation of the picolinic acid at C-3, but from a successive process of C-3 hydroxylation of the piperideine-2-carboxylic acid and tautomerization of the produced 3-hydroxyl dihydropicolinic acid. Therefore, this study unveils the unusual assembly logic of 3-HPA and sheds light on the potential of engineering the 3-HPA pathway for generating novel pyridine-based building blocks.

Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils

In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.

Catabolism of 2-Hydroxypyridine by Burkholderia sp. Strain MAK1: a 2-Hydroxypyridine 5-Monooxygenase Encoded by hpdABCDE Catalyzes the First Step of Biodegradation

Microbial degradation of 2-hydroxypyridine usually results in the formation of a blue pigment (nicotine blue). In contrast, the Burkholderia sp. strain MAK1 bacterium utilizes 2-hydroxypyridine without the accumulation of nicotine blue. This scarcely investigated degradation pathway presumably employs 2-hydroxypyridine 5-monooxygenase, an elusive enzyme that has been hypothesized but has yet to be identified or characterized. The isolation of the mutant strain Burkholderia sp. MAK1 ΔP5 that is unable to utilize 2-hydroxypyridine has led to the identification of a gene cluster (designated hpd) which is responsible for the degradation of 2-hydroxypyridine. The activity of 2-hydroxypyridine 5-monooxygenase has been assigned to a soluble diiron monooxygenase (SDIMO) encoded by a five-gene cluster (hpdA, hpdB, hpdC, hpdD, and hpdE). A 4.5-kb DNA fragment containing all five genes has been successfully expressed in Burkholderia sp. MAK1 ΔP5 cells. We have proved that the recombinant HpdABCDE protein catalyzes the enzymatic turnover of 2-hydroxypyridine to 2,5-dihydroxypyridine. Moreover, we have confirmed that emerging 2,5-dihydroxypyridine is a substrate for HpdF, an enzyme similar to 2,5-dihydroxypyridine 5,6-dioxygenases that are involved in the catabolic pathways of nicotine and nicotinic acid. The proteins and genes identified in this study have allowed the identification of a novel degradation pathway of 2-hydroxypyridine. Our results provide a better understanding of the biodegradation of pyridine derivatives in nature. Also, the discovered 2-hydroxypyridine 5-monooxygenase may be an attractive catalyst for the regioselective synthesis of various N-heterocyclic compounds.IMPORTANCE The degradation pathway of 2-hydroxypyridine without the accumulation of a blue pigment is relatively unexplored, as, to our knowledge, no genetic data related to this process have ever been presented. In this paper, we describe genes and enzymes involved in this little-studied catabolic pathway. This work provides new insights into the metabolism of 2-hydroxypyridine in nature. A broad-range substrate specificity of 2-hydroxypyridine 5-monooxygenase, a key enzyme in the degradation, makes this biocatalyst attractive for the regioselective hydroxylation of pyridine derivatives.

Oxyfunctionalization of pyridine derivatives using whole cells of Burkholderia sp. MAK1

Pyridinols and pyridinamines are important intermediates with many applications in chemical industry. The pyridine derivatives are in great demand as synthons for pharmaceutical products. Moreover, pyridines are used either as biologically active substances or as building blocks for polymers with unique physical properties. Application of enzymes or whole cells is an attractive strategy for preparation of hydroxylated pyridines since the methods for chemical synthesis of pyridinols, particularly aminopyridinols, are usually limited or inefficient. Burkholderia sp. MAK1 (DSM102049), capable of using pyridin-2-ol as the sole carbon and energy source, was isolated from soil. Whole cells of Burkholderia sp. MAK1 were confirmed to possess a good ability to convert different pyridin-2-amines and pyridin-2-ones into their 5-hydroxy derivatives. Moreover, several methylpyridines as well as methylated pyrazines were converted to appropriate N-oxides. In conclusion, regioselective oxyfunctionalization of pyridine derivatives using whole cells of Burkholderia sp. MAK1 is a promising method for the preparation of various pyridin-5-ols and pyridin-N-oxides.

Mechanism of the 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase flavoprotein from Pseudomonas putida S16

6-Hydroxy-3-succinoyl-pyridine (HSP) 3-monooxygenase (HspB), a flavoprotein essential to the pyrrolidine pathway of nicotine degradation, catalyzes pyridine-ring β-hydroxylation, resulting in carbon-carbon cleavage and production of 2,5-dihydroxypyridine. Here, we generated His6-tagged HspB in Escherichia coli, characterized the properties of the recombinant enzyme, and investigated its mechanism of catalysis. In contrast to conclusions reported previously, the second product of the HspB reaction was shown to be succinate, with isotope labeling experiments providing direct evidence that the newly introduced oxygen atom of succinate is derived from H2O. Phylogenetic analysis reveals that HspB is the most closely related to two p-nitrophenol 4-monooxygenases, and the experimental results exhibit that p-nitrophenol is a substrate of HspB. The reduction of HspB (with maxima at 375 and 460 nm, and a shoulder at 485 nm) by NADH was followed by stopped-flow spectroscopy, and the rate constant for reduction was shown to be stimulated by HSP. Reduced HspB reacts with oxygen to form a C(4a)-(hydro)peroxyflavin intermediate with an absorbance maximum at ∼400 nm within the first few milliseconds before converting to the oxidized flavoenzyme species. The formed C(4a)-hydroperoxyflavin intermediate reacts with HSP to form an intermediate that hydrolyzes to the products 2,5-dihydroxypyridine and succinate. The investigation on the catalytic mechanism of a flavoprotein pyridine-ring β-position hydroxylase provides useful information for the biosynthesis of pyridine derivatives.

UV photolysis for accelerating pyridine biodegradation

Pyridine, a nitrogen-containing heterocyclic compound, is slowly biodegradable, and coupling biodegradation with UV photolysis is a potential means to accelerate its biotransformation and mineralization. The initial steps of pyridine biodegradation involve mono-oxygenation reactions that have molecular oxygen and an intracellular electron carrier as cosubstrates. We employed an internal circulation baffled biofilm reactor for pyridine biodegradation following three protocols: direct biodegradation (B), biodegradation after photolysis (P+B), and biodegradation with succinic acid added (B+S). Succinic acid was the main UV-photolysis product from pyridine, and its catabolic oxidation generates internal electron carriers that may accelerate the initial steps of pyridine biodegradation. Compared with direct biodegradation of pyridine (B), the removal rate for the same concentration of photolyzed pyridine (P+B) was higher by 15 to 43%, depending on the initial pyridine concentrations (increasing through the range of 130 to 310 mg/L). Adding succinic acid alone (B+S) gave results similar to P+B, which supports that succinic acid was the main agent for accelerating the pyridine biodegradation rate. In addition, protocols P+B and B+S were similar in terms of increasing pyridine mineralization over 10 h: 84% and 87%, respectively, which were higher than with protocol B (72%). The positive impact of succinic acid-whether added directly or produced via UV photolysis-confirms that its catabolism, which produced intracellular electron carriers, accelerated the initial steps of pyridine biotransformation.