Detection and characterisation of catechol 2,3-dioxygenase in an indigenous soil Pseudomonad by MALDI-TOF MS using a column separation

Shape-function of a novel metapyrocatechase, RW4-MPC: Metagenomics to SAXS data based insight into deciphering regulators of function

The oxygenases have attracted considerable attention in enzyme-mediated bioremediation of xenobiotic compounds due to their high specificity, cost-effectiveness, and targeted field applications. Here, we performed a functional metagenomics approach to cope with cultivability limitations to isolate a novel extradiol dioxygenase. Fosmid clone harboring dioxygenase gene was sequenced and analyzed by bioinformatics tools. One ring-cleaving dioxygenase RW4-MPC (metapyrocatechase) was purified and characterized to examine its degradation efficiency. The RW4-MPC was significantly active in the temperature and pH range of 5 to 40 °C, and 7-10, respectively, with an optimum temperature of 25 °C and pH 8. To gain insight into observed differential activity, Small-Angle X-ray Scattering (SAXS) data of the protein samples were analyzed, which brought forth that the RW4-MPC molecules form tight globular tetramers in solution. This native association was stable till 35 °C, and protein started to associate at higher temperatures, explaining heat-induced loss of function. Similarly, RW4-MPC aggregated or lost globular profile below pH 7 or at pH 10, respectively. The kinetic parameters showed the six folds high catalytic efficiency of RW4-MPC towards 2,3-dihydroxy biphenyl than catechol and its derivatives. RW4-MPC molecules showed remarkable retention of functionality in hypersaline conditions with more than 70% activity in a buffer having 3 M NaCl concentration. In concordance, SAXS data analysis showed retention of functional shape profile in hypersaline conditions. The halotolerant and oxygen insensitive nature of this enzyme makes it a potential candidate for bioremediation.

Polyhydroxyalkanoate (PHA) Production in Pseudomonas sp. phDV1 Strain Grown on Phenol as Carbon Sources

Pseudomonas strains have a variety of potential uses in bioremediation and biosynthesis of biodegradable plastics. Pseudomonas sp. strain phDV1, a Gram-negative phenol degrading bacterium, has been found to utilize monocyclic aromatic compounds as sole carbon source via the meta-cleavage pathway. The degradation of aromatic compounds comprises an important step in the removal of pollutants. The present study aimed to investigate the ability of the Pseudomonas sp. strain phDV1 to produce polyhydroxyalkanoates (PHAs) and examining the effect of phenol concentration on PHA production. The bacterium was cultivated in minimal medium supplemented with different concentrations of phenol ranging from 200-600 mg/L. The activity of the PHA synthase, the key enzyme which produces PHA, was monitored spectroscopically in cells extracts. Furthermore, the PHA synthase was identified by mass spectrometry in cell extracts analyzed by SDS-PAGE. Transmission electron micrographs revealed abundant electron-transparent intracellular granules. The isolated biopolymer was confirmed to be polyhydroxybutyrate (PHB) by FTIR, NMR and MALDI-TOF/TOF analyses. The ability of strain Pseudomonas sp. phDV1 to remove phenol and to produce PHB makes the strain a promising biocatalyst in bioremediation and biosynthesis of biodegradable plastics.

Proteomic Characterization of the Pseudomonas sp. Strain phDV1 Response to Monocyclic Aromatic Compounds

The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here, Pseudomonas sp. strain phDV1, a gram-negative bacterium that is selected for its ability to degrade aromatic compounds is studied. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carbon source, the proteome of this strain is analyzed in the presence of succinate, phenol, and o-, m-, and p-cresol as the sole carbon source. As a reference proteome, the bacteria are grown in succinate and then compared with the respective proteomes of bacteria grown on phenol and different cresols. In total, 2295 proteins are identified; 1908 proteins are used for quantification between different growth conditions. The carbon source affects the synthesis of enzymes related to aromatic compound degradation and in particular the enzyme involved in the meta-pathway of monocyclic aromatic compounds degradation. In addition, proteins involved in the production of polyhydroxyalkanoate (PHA), an attractive biomaterial, show higher abundance in the presence of monocyclic aromatic compounds. The results provide, for the first time, comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.

Complete Genome Sequence of Pseudomonas sp. Strain phDV1, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons

Pseudomonas sp. strain phDV1 is a Gram-negative bacterium capable of degrading aromatic hydrocarbons. Here, we present the complete genome sequence of this strain, which consists of 4,727,682 bp, with a 62.3% G+C content and 4,574 genes. Multiple genes responsible for the degradation of aromatics are present in this strain.

Antioxidant enzymes are induced by phenol in the marine microalga Lingulodinium polyedrum

Knowing the impacts of different anthropogenic activities on ecosystems promotes preservation of aquatic organisms. Aiming to facilitate the identification of polluted or contaminated areas, the study of microalga Lingulodinium polyedrum in phenol-containing medium comprises the determination of toxic and metabolic phenol effects, featuring a possible use of this microorganism as bioindicator for this pollutant. Marine microalga L. polyedrum exposure to phenol increases superoxide dismutase (SOD) and catalase (CAT) activities. The 20% and 50% inhibitory concentrations (IC20 and IC50) of cells exposed to phenol were 40 μmol L(-1) and 120 μmol L(-1), respectively. Phenol biodegradation by L. polyedrum was 0.02 μmol h(-1)cell(-1), and its biotransformation was catalyzed by glutathione S-transferase (GST), phenol hydroxylase and catechol 2,3-dihydroxygenase metabolic pathways. Phenol exposure produced the metabolites 2-hydroxymuconic semialdehyde acid, 1,2-dihydroxybenzene (catechol), and 2-oxo-4-pentenoic acid; also, it induced the activity of key antioxidant biomarker enzymes SOD and CAT by three folds compared to that in the controls. Further, phenol decreased the glutathione/oxidized glutathione ratio (GSH/GSSG), highlighting the effective glutathione oxidation in L. polyedrum. Overall, our results suggest that phenol alters microalga growth conditions and microalgae are sensitive bioindicators to pollution by phenol in marine environments.

Comparison of the membrane subproteomes during growth of a new pseudomonas strain on lysogeny broth medium, glucose, and phenol

Study of the bacterial membrane proteome is a field of growing interest in the research of nutrient transport and processing. Pseudomonas sp. strain phDV1, a Gram-negative bacterium selected for its ability to degrade aromatic compounds, was monitored under different growth substrate conditions, using lysogeny broth medium (LB), glucose, and phenol as sole carbon source. The aim of this study was to characterize the membrane subproteomes of the Pseudomonas strain by proteomic means to assess the protein composition of this subcellular compartments, which appears fundamental for the biodegradation of aromatic compounds. A total number of 129 different proteins have been identified by MALDI-TOF/TOF, 19 of which are membrane proteins that belong to the inner membrane and 10 that belong to the outer membrane. Two membrane proteins were only expressed in the presence of the aromatic substrate. We identified a membrane protein involved in aromatic hydrocarbon degradation as well as a probable porin which may, in fact, function as an aromatic compound-specific porin. Although the presence of different transporters have been reported for different aromatic compounds such as toluene and benzoic acid, to our knowledge, these are the first phenol-inducible membrane transporters identified.

Novel organization of catechol meta pathway genes in the nitrobenzene degrader Comamonas sp. JS765 and its evolutionary implication

The catechol meta cleavage pathway is one of the central metabolic pathways for the degradation of aromatic compounds. A novel organization of the pathway genes, different from that of classical soil microorganisms, has been observed in Sphingomonas sp HV3 and Pseudomonas sp. DJ77. In a Comamonas sp. JS765, cdoE encoding catechol 2,3-dioxygenase shares a common ancestry only with tdnC of a Pseudomonas putida strain, while codG encoding 2-hydroxymuconic semialdehyde dehydrogenase shows a higher degree of similarity to those genes in classical bacteria. Located between cdoE and cdoG are several putative genes, whose functions are unknown. These genes are not found in meta pathway operons of other microorganisms with the exception of cdoX2, which is similar to cmpX in strain HV3. Therefore, the gene cluster in JS765 reveals a third type of gene organization of the meta pathway.

Identification of inducible protein complexes in the phenol degrader Pseudomonas sp. strain phDV1 by blue native gel electrophoresis and mass spectrometry

Pseudomonas sp. strain phDV1, being a phenol degrading bacterium, has been found to utilize phenol as sole carbon source via the meta pathway. Blue native polyacrylamide gel electrophoresis (BN-PAGE) is widely used for the analysis of oligomeric state and molecular mass non-dissociated protein complexes. In this study, a number of proteomic techniques were used to investigate the oligomeric state enzymes involved in the aromatic degradation pathway. In particular, the Pseudomonas sp. strain phDV1 proteome was monitored under two different growth substrate conditions, using glucose or phenol as sole carbon source. The protein complexes map was compared by BN-PAGE after fractionation by sucrose density centrifugation of the cell extracts. Multiple differences were detected. Further, analysis and identification of the subunit composition of these complexes was carried out using MALDI-TOF MS, allowing the identification of 49 proteins. Additionally, functional information regarding protein-protein interactions was assembled, by coupling 2-D BN-PAGE with MALDI-TOF MS. Application of this functional proteomics method resulted in an higher number of the identified proteins.