Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily

Genome analysis for the identification of genes involved in phenanthrene biodegradation pathway in Stenotrophomonas indicatrix CPHE1. Phenanthrene mineralization in soils assisted by integrated approaches

Phenanthrene (PHE) is a highly toxic compound, widely present in soils. For this reason, it is essential to remove PHE from the environment. Stenotrophomonas indicatrix CPHE1 was isolated from an industrial soil contaminated by polycyclic aromatic hydrocarbons (PAHs) and was sequenced to identify the PHE degrading genes. Dioxygenase, monooxygenase, and dehydrogenase gene products annotated in S. indicatrix CPHE1 genome were clustered into different trees with reference proteins. Moreover, S. indicatrix CPHE1 whole-genome sequences were compared to genes of PAHs-degrading bacteria retrieved from databases and literature. On these basis, reverse transcriptase-polymerase chain reaction (RT-PCR) analysis pointed out that cysteine dioxygenase (cysDO), biphenyl-2,3-diol 1,2-dioxygenase (bphC), and aldolase hydratase (phdG) were expressed only in the presence of PHE. Therefore, different techniques have been designed to improve the PHE mineralization process in five PHE artificially contaminated soils (50 mg kg^-1), including biostimulation, adding a nutrient solution (NS), bioaugmentation, inoculating S. indicatrix CPHE1 which was selected for its PHE-degrading genes, and the use of 2-hydroxypropyl-β-cyclodextrin (HPBCD) as a bioavailability enhancer. High percentages of PHE mineralization were achieved for the studied soils. Depending on the soil, different treatments resulted to be successful; in the case of a clay loam soil, the best strategy was the inoculation of S. indicatrix CPHE1 and NS (59.9% mineralized after 120 days). In sandy soils (CR and R soils) the highest percentage of mineralization was achieved in presence of HPBCD and NS (87.3% and 61.3%, respectively). However, the combination of CPHE1 strain, HPBCD, and NS showed to be the most efficient strategy for sandy and sandy loam soils (LL and ALC soils showed 35% and 74.6%, respectively). The results indicated a high degree of correlation between gene expression and the rates of mineralization.

Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

BACKGROUND

Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear.

RESULTS

Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway.

CONCLUSIONS

Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.

A Type 1 Aldolase, NahE, Catalyzes a Stereoselective Nitro-Michael Reaction: Synthesis of β-Aryl-γ-nitrobutyric Acids

Michael addition reactions are highly useful in organic synthesis and are commonly accomplished using organocatalysts. However, the corresponding biocatalytic Michael additions are rare, typically lack synthetically useful substrate scope, and suffer from low stereoselectivity. Herein we report a biocatalytic nitro-Michael addition, catalyzed by NahE, that proceeds with low catalyst loading at room temperature in moderate to excellent enantioselectivity and high yields. A series of β-nitrostyrenes reacted with pyruvate in the presence of NahE to give, after oxidative decarboxylation, β-aryl-γ-nitrobutyric acids in up to 99 % yield without need for chromatography, providing a simple preparative-scale route to chiral GABA analogues. This reaction represents the first example of an aldolase displaying promiscuous Michaelase activity and opens the use of nitroalkenes in place of aldehydes as substrates for aldolases.

A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway

NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (H, OH, or CO2-) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is in a bacterial degradative pathway for naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. A crystal structure of the selenomethionine derivative of NahE shows these active site elements along with nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on catalysis. The results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. Changing Tyr155 to Phe and Asn157 to Ala also hinders catalysis, and the effects fall in between these extremes. These observations are put into a structural context using a crystal structure of the Schiff base of the reaction intermediate. Trapping experiments with substrate, Na(CN)BH3, and wild type enzyme and selected mutants mostly paralleled the kinetic analysis, and identified two salicylaldehyde-modified lysines: the active site lysine (Lys183) and one outside the active site (Lys279). The latter could be responsible for the observed inhibition of NahE by salicylaldehyde. Together, the results provide new insights into the NahE-catalyzed reaction.

A Review of Pyrene Bioremediation Using Mycobacterium Strains in a Different Matrix

Polycyclic aromatic hydrocarbons are compounds with 2 or more benzene rings, and 16 of them have been classified as priority pollutants. Among them, pyrene has been found in higher concentrations than recommended, posing a threat to the ecosystem. Many bacterial strains have been identified as pyrene degraders. Most of them belong to Gram-positive strains such as Mycobacterium sp. and Rhodococcus sp. These strains were enriched and isolated from several sites contaminated with petroleum products, such as fuel stations. The bioremediation of pyrene via Mycobacterium strains is the main objective of this review. The scattered data on the degradation efficiency, formation of pyrene metabolites, bio-toxicity of pyrene and its metabolites, and proposed degradation pathways were collected in this work. The study revealed that most of the Mycobacterium strains were capable of degrading pyrene efficiently. The main metabolites of pyrene were 4,5-dihydroxy pyrene, phenanthrene-4,5-dicarboxylate, phthalic acid, and pyrene-4,5-dihydrodiol. Some metabolites showed positive results for the Ames mutagenicity prediction test, such as 1,2-phenanthrenedicarboxylic acid, 1-hydroxypyrene, 4,5-dihydropyrene, 4-phenanthrene-carboxylic acid, 3,4-dihydroxyphenanthrene, monohydroxy pyrene, and 9,10-phenanthrenequinone. However, 4-phenanthrol showed positive results for experimental and prediction tests. This study may contribute to enhancing the bioremediation of pyrene in a different matrix.

Preparation of dihydroxy polycyclic aromatic hydrocarbons and activities of two dioxygenases in the phenanthrene degradative pathway

Dihydroxy phenanthrene, fluoranthene, and pyrene derivatives are intermediates in the bacterial catabolism of the corresponding parent polycyclic aromatic hydrocarbon (PAH). Ring-opening of the dihydroxy species followed by a series of enzyme-catalyzed reactions generates metabolites that funnel into the Krebs Cycle with the eventual production of carbon dioxide and water. One complication in delineating these pathways and harnessing them for useful purposes is that the initial enzymatic processing produces multiple dihydroxy PAHs with multiple ring opening possibilities and products. As part of a systematic effort to address this issue, eight dihydroxy species were synthesized and characterized as the dimethoxy or diacetate derivatives. Several dihydroxy compounds were examined with two dioxygenases in the phenanthrene degradative pathway in Mycobacterium vanbaalenii PYR-1. One, 3,4-dihydroxyphenanthrene, was processed by PhdF with a k_cat/K_m of 6.0 × 10⁶ M^-1s^-1, a value that is consistent with the annotated function of PhdF in the pathway. PhdI processed 1-hydroxy-2-naphthoate with a k_cat/K_m of 3.1 × 10⁵ M^-1s^-1, which is also consistent with the proposed role in the pathway. The observations provide the first biochemical evidence for these two reactions in M. vanbaalenii PYR-1 and, to the best of our knowledge, the first biochemical evidence for the reaction of PhdF with 3,4-dihydroxyphenanthrene. Although PhdF is upregulated in the presence of pyrene, it did not process two dihydroxypyrenes. Methodology was developed for product analysis of the extradiol dioxygenases.