Diversity of the Aromatic-Ring-Hydroxylating Dioxygenases in the Monoaromatic Hydrocarbon Degraders Held by a Common Ancestor

The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis

Pyrene is a pollutant in the environment and affects the health of living organisms. It is important to understand microbial-mediated pyrene resistance and the related molecular mechanisms due to its toxicity and biodegradability. Due to the unclear response mechanisms of bacteria to PAHs, this study detected the transcriptional changes in Escherichia coli under different pyrene concentrations using transcriptome sequencing technology. Global transcriptome analysis showed that the number of differentially expressed genes (DEGs) in multiple metabolic pathways increased with increasing concentrations of pyrene. In addition, the effects and toxicity of pyrene on Escherichia coli mainly included the up-regulation and inhibition of genes related to carbohydrate metabolism, membrane transport, sulfate reduction, various oxidoreductases, and multidrug efflux pumps. Moreover, we also constructed an association network between significantly differentially expressed sRNAs and key genes and determined the regulatory relationship and key genes of Escherichia coli under pyrene stress. Our study utilized pyrene as an exogenous stress substance to investigate the possible pathways of the bacterial stress response. In addition, this study provides a reference for other related research and serves as a foundation for future research.

Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons

Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.

DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation

Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.

The many faces of Raoultella spp

Raoultella genus consists of Gram-negative, aerobic, encapsulated and non-motile rods. The name of the genus derives from the name of the French bacteriologist Raoul. Currently, four species belong to the genus: R. planticola, R. ornithinolytica, R. terrigena and R. electrica. The standard biochemical test used to identify Raoultella genus should be supplemented with additional tests, because of the close relationship between the genera Raoultella and Klebsiella. In 2001 Klebsiella planticola, K. ornithinolytica and K. terrigena were re-classified to new genus Raoultella. Re-classification was based on 16S rRNA sequence and rpoB, gyrA and gyrB genes. An alternative to phenotypic identification may be mass spectrometry or genetic methods (16s rRNA). These bacteria are commonly associated with natural environments (plants, water, soil). Raoultella spp. rods are not a highly virulent pathogen. Their virulence factors include polysaccharide capsule, fimbriae, siderophores, toxins and ability to form a biofilm. It has been shown that Raoultella spp. may colonize the gastrointestinal and upper respiratory tract in humans and cause cholangitis and lung infections. The literature also includes works on the antimicrobial activity of Raoultella rods and the possibility of using them in the environment protection. This review summarizes the current knowledge of Raoultella species identification, virulence and the possibility of using them in the protection of the environment.