Benzoate degradation by Rhodococcus opacus 1CP after dormancy: Characterization of dioxygenases involved in the process

Molecular evaluation of the metabolism of estrogenic di(2-ethylhexyl) phthalate in Mycolicibacterium sp

BACKGROUND

Di(2-ethylhexyl) phthalate (DEHP) is a widely detected plasticizer and a priority pollutant of utmost concern for its adverse impact on humans, wildlife and the environment. To eliminate such toxic burden, biological processes are the most promising ways to combat rampant environmental insults under eco-friendly conditions. The present study investigated the biochemical and molecular assessment of the catabolic potential of Mycolicibacterium sp. strain MBM in the assimilation of estrogenic DEHP.

RESULTS

A detailed biochemical study revealed an initial hydrolytic pathway of degradation for DEHP followed by the assimilation of hydrolyzed phthalic acid and 2-ethylhexanol to TCA cycle intermediates. Besides the inducible nature of DEHP-catabolic enzymes, strain MBM can efficiently utilize various low- and high-molecular-weight phthalate diesters and can grow under moderately halotolerant conditions. Whole genome sequence analysis exhibited a genome size of 6.2 Mb with a GC content of 66.51% containing 6,878 coding sequences, including multiple genes, annotated as relevant to the catabolism of phthalic acid esters (PAEs). Substantiating the annotated genes through transcriptome assessment followed by RT-qPCR analysis, the possible roles of upregulated genes/gene clusters in the metabolism of DEHP were revealed, reinforcing the biochemical pathway of degradation at the molecular level.

CONCLUSIONS

A detailed co-relation of biochemical, genomic, transcriptomic and RT-qPCR analyses highlights the PAE-degrading catabolic machineries in strain MBM. Further, due to functional attributes in the salinity range of both freshwater and seawater, strain MBM may find use as a suitable candidate in the bioremediation of PAEs.

Microbial Biosensor for Characterization of a Microorganism: A Review focusing on the Biochemical Activity of Microbial Cells

Express assessment of the biochemical activity of microorganisms is important in both applied and fundamental research. A laboratory model of a microbial electrochemical sensor formed on the basis of the culture of interest is a device that provides rapidly information about the culture and is cost effective, simple to fabricate and easy to use. This paper describes the application of laboratory models of microbial sensors in which the Clark-type oxygen electrode was used as a transducer. The formation of the models of the reactor microbial sensor (RMS) and the membrane microbial sensor (MMS) and the formation of the response of biosensors are compared. RMS and MMS are based on intact or immobilized microbial cells, respectively. For MMS, the response of biosensor is caused both by the process of transport of substrate into microbial cells and by the process of the initial metabolism of substrate; and only initial substrate metabolism triggers the RMS response. The details of the application of biosensors for the study of allosteric enzymes and inhibition by substrate are discussed. For inducible enzymes, special attention is paid to the induction of microbial cells. This article addresses current problems related to implementation of the biosensor approach and discusses the ways how to overcome these problems.

Genome Functional Analysis of the Psychrotrophic Lignin-Degrading Bacterium Arthrobacter sp. C2 and the Role of DyP in Catalyzing Lignin Degradation

In the cold regions of China, lignin-rich corn straw accumulates at high levels due to low temperatures. The application of psychrotrophic lignin-degrading bacteria should be an effective means of overcoming the low-temperature limit for lignin degradation and promoting the utilization of corn straw. However, this application is limited by the lack of suitable strains for decomposition of lignin; furthermore, the metabolic mechanism of psychrotrophic lignin-degrading bacteria is unclear. Here, the whole genome of the psychrotrophic lignin-degrading bacterium Arthrobacter sp. C2, isolated in our previous work, was sequenced. Comparative genomics revealed that C2 contained unique genes related to lignin degradation and low-temperature adaptability. DyP may participate in lignin degradation and may be a cold-adapted enzyme. Moreover, DyP was proven to catalyze lignin Cα-Cβ bond cleavage. Deletion and complementation of the DyP gene verified its ability to catalyze the first-step reaction of lignin degradation. Comparative transcriptomic analysis revealed that the transcriptional expression of the DyP gene was upregulated, and the genetic compensation mechanism allowed C2ΔDyP to degrade lignin, which provided novel insights into the survival strategy of the psychrotrophic mutant strain C2ΔdyP. This study improved our understanding of the metabolic mechanism of psychrotrophic lignin-degrading bacteria and provided potential application options for energy-saving production using cold-adapted lignin-degrading enzymes.

Rhodococcus as A Versatile Biocatalyst in Organic Synthesis

The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry are keen on finding and developing novel enzymes capable of performing otherwise impossible or challenging reactions. The diverse genus Rhodococcus offers a multitude of promising enzymes, which therefore makes it one of the key bacterial hosts in many areas of research. This review focused on the broad utilization potential of the genus Rhodococcus in organic chemistry, thereby particularly highlighting the specific enzyme classes exploited and the reactions they catalyze. Additionally, close attention was paid to the substrate scope that each enzyme class covers. Overall, a comprehensive overview of the applicability of the genus Rhodococcus is provided, which puts this versatile microorganism in the spotlight of further research.

Simultaneous 3-/4-Hydroxybenzoates Biodegradation and Arsenite Oxidation by Hydrogenophaga sp. H7

Aromatic compounds and arsenic (As) often coexist in the environment. As(III)-oxidizing bacteria can oxidize the more toxic As(III) into the less toxic As(V), and As(V) is easily removed. Microorganisms with the ability to degrade aromatic compounds and oxidize arsenite [As(III)] may have strong potential to remediate co-contaminated water. In this study, a Gram-negative bacterium Hydrogenophaga sp. H7 was shown to simultaneously degrade 3-hydroxybenzoate (3-HBA) or 4-HBA (3-/4-HBA) and oxidize arsenite [As(III)] to arsenate [As(V)] during culture. Notably, the addition of As(III) enhanced the degradation rates of 3-/4-HBA, while the addition of 3-/4-HBA resulted in a slight delay in As(III) oxidation. Use of a 1% bacterial culture in combination with FeCl₃ could completely degrade 250 mg/L 3-HBA or 4-HBA and remove 400 μM As(III) from simulated lake water within 28 h. Genomic analysis revealed the presence of As(III) oxidation/resistance genes and two putative 3-/4-HBA degradation pathways (the protocatechuate 4,5-dioxygenase degradation pathway and the catechol 2,3-dioxygenase degradation pathway). Comparative proteomics suggested that strain H7 degraded 4-HBA via the protocatechuate 4,5-dioxygenase degradation pathway in the absence of As(III); however, 4-HBA could be degraded via the catechol 2,3-dioxygenase degradation pathway in the presence of As(III). In the presence of As(III), more NADH was produced by the catechol 2,3-dioxygenase degradation pathway and/or by As(III) oxidation, which explained the enhancement of bacterial 4-HBA degradation in the presence of As(III). In addition, the key gene dmpB, which encodes catechol 2,3-dioxygenase in the catechol 2,3-dioxygenase degradation pathway, was knocked out, which resulted in the disappearance of As(III)-enhanced bacterial 4-HBA degradation from the dmpB mutant strain, which further confirmed that As(III) enhancement of 4-HBA degradation was due to the utilization of the catechol 2,3-dioxygenase pathway. These discoveries indicate that Hydrogenophaga sp. H7 has promise for the application to the removal of aromatic compounds and As co-contamination and reveal the relationship between As oxidation and aromatic compound degradation.

Kinetics of interaction between substrates/substrate analogs and benzoate 1,2-dioxygenase from benzoate-degrading Rhodococcus opacus 1CP

Benzoate 1,2-dioxygenase (BDO) of Rhodococcus opacus 1CP, which carried out the initial attack on benzoate, was earlier shown to be the enzyme with a narrow substrate specificity. A kinetics of interaction between benzoate 1,2-dioxygenase and substituted benzoates was assessed taking into account the enlarged list of the type of inhibition and using whole cells grown on benzoate. The type of inhibition was determined and the constants of a reaction of BDO with benzoate in the presence of 2-chlorobenzoate (2CBA), 3,5-dichlorobenzoate (3,5DCBA), and 3-methylbenzoate (3MBA) were calculated. For 2CBA and 3MBA, the types of inhibition were classified as biparametrically disсoordinated inhibition and transient inhibition (from activation towards inhibition), respectively. The process of not widely recognized pseudoinhibition of a BDO reaction with benzoate by 3,5DCBA was assessed by the vector method for the representation of enzymatic reactions. Ki value was determined for 2CBA, 3MBA, and 3,5DCBA as 337.5, 870.3, and 14.7 μM, respectively.

Dioxygenases of Chlorobiphenyl-Degrading Species Rhodococcus wratislaviensis G10 and Chlorophenol-Degrading Species Rhodococcus opacus 1CP Induced in Benzoate-Grown Cells and Genes Potentially Involved in These Processes

Dioxygenases induced during benzoate degradation by the actinobacterium Rhodococcus wratislaviensis G10 strain degrading haloaromatic compounds were studied. Rhodococcus wratislaviensis G10 completely degraded 2 g/liter benzoate during 30 h and 10 g/liter during 200 h. Washed cells grown on benzoate retained respiration activity for more than 90 days, and a high activity of benzoate dioxygenase was recorded for 10 days. Compared to the enzyme activities with benzoate, the activity of benzoate dioxygenases was 10-30% with 13 of 35 substituted benzoate analogs. Two dioxygenases capable of cleaving the aromatic ring were isolated and characterized: protocatechuate 3,4-dioxygenase and catechol 1,2-dioxygenase. Catechol inhibited the activity of protocatechuate 3,4-dioxygenase. Protocatechuate did not affect the activity of catechol 1,2-dioxygenase. A high degree of identity was shown by MALDI-TOF mass spectrometry for protein peaks of the R. wratislaviensis G10 and Rhodococcus opacus 1CP cells grown on benzoate or LB. DNA from the R. wratislaviensis G10 strain was specifically amplified using specific primers to variable regions of genes coding α- and β-subunits of protocatechuate 3,4-dioxygenase and to two genes of the R. opacus 1CP coding catechol 1,2-dioxygenase. The products were 99% identical with the corresponding regions of the R. opacus 1CP genes. This high identity (99%) between the genes coding degradation of aromatic compounds in the R. wratislaviensis G10 and R. opacus 1CP strains isolated from sites of remote location (1400 km) and at different time (20-year difference) indicates a common origin of biodegradation genes of these strains and a wide distribution of these genes among rhodococci.