Jong-Su Seo

Bacterial Degradation of Aromatic Compounds

Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

Degradation of phenanthrene by Burkholderia sp. C3 : initial 1,2-and 3,4-dioxygenation and meta-and ortho-cleavage of naphthalene-1,2-diol

Burkholderia sp. C3 was isolated from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Hilo, Hawaii, USA, and studied for its degradation of phenanthrene as a sole carbon source. The initial 3,4-C dioxygenation was faster than 1,2-C dioxygenation in the first 3-day culture. However, 1-hydroxy-2-naphthoic acid derived from 3,4-C dioxygenation degraded much slower than 2-hydroxy-1-naphthoic acid derived from 1,2-C dioxygenation. Slow degradation of 1-hydroxy-2-naphthoic acid relative to 2-hydroxy-1-naphthoic acid may trigger 1,2-C dioxygenation faster after 3xa0days of culture. High concentrations of 5,6-␣and 7,8-benzocoumarins indicated that meta-cleavage was the major degradation mechanism of phenanthrene-1,2- and -3,4-diols. Separate cultures with 2-hydroxy-1-naphthoic acid and 1-hydroxy-2-naphthoic acid showed that the degradation rate of the former to naphthalene-1,2-diol was much faster than that of the latter. The two upper metabolic pathways of phenanthrene are converged into naphthalene-1,2-diol that is further metabolized to 2-carboxycinnamic acid and 2-hydroxybenzalpyruvic acid by ortho- and meta-cleavages, respectively. Transformation of naphthalene-1,2-diol to 2-carboxycinnamic acid by this strain represents the first observation of ortho-cleavage of two rings-PAH-diols by a Gram-negative species.

Degradation pathways of phenanthrene by Sinorhizobium sp. C4.

Sinorhizobium sp. C4 was isolated from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Hilo, HI, USA. This isolate can utilize phenanthrene as a sole carbon source. Sixteen metabolites of phenanthrene were isolated and identified, and the metabolic map was proposed. Degradation of phenanthrene was initiated by dioxygenation on 1,2- and 3,4-C, where the 3,4-dioxygenation was dominant. Subsequent accumulation of 5,6- and 7,8-benzocoumarins confirmed dioxygenation on multiple positions and extradiol cleavage of corresponding diols. The products were further transformed to 1-hydroxy-2-naphthoic acid and 2-hydroxy-1-naphthoic acid then to naphthalene-1,2-diol. In addition to the typical degradation pathways, intradiol cleavage of phenanthrene-3,4-diol was proposed based on the observation of naphthalene-1,2-dicarboxylic acid. Degradation of naphthalene-1,2-diol proceeded through intradiol cleavage to produce trans-2-carboxycinnamic acid. Phthalic acid, 4,5-dihydroxyphthalic acid, and protocatechuic acid were identified as probable metabolites of trans-2-carboxycinnamic acid, but no trace salicylic acid or its metabolites were found. This is the first detailed study of PAH metabolism by a Sinorhizobium species. The results give a new insight into microbial degradation of PAHs.

Synthesis of Bacterial Metabolites of Polycyclic Aromatic Hydrocarbons: Benzochromenones, o‐Carboxyvinylnaphthoates, and o‐Substituted Aryl‐α‐Oxobutenoates

Abstract Bacterial metabolites of phenanthrene and anthracene include benzochromenones, o‐carboxyvinylnaphthoates, and o‐substituted aryl α‐oxobutenoates, which were synthesized with the Wittig reaction, the Heck reaction, and coupling of aromatic aldehyde with pyruvate.

Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N -methylcarbamates

Burkholderia sp. C3, an efficient polycyclic aromatic hydrocarbon degrader, can utilize nine of the ten N-methylcarbamate insecticides including carbaryl as a sole source of carbon. Rapid hydrolysis of carbaryl in C3 is followed by slow catabolism of the resulting 1-naphthol. This study focused on metabolomes and proteomes in C3 cells utilizing carbaryl in comparison to those using glucose or nutrient broth. Sixty of the 867 detected proteins were involved in primary metabolism, adaptive sensing and regulation, transport, stress response, and detoxification. Among the 41 proteins expressed in response to carbaryl were formate dehydrogenase, aldehyde-alcohol dehydrogenase and ethanolamine utilization protein involved in one carbon metabolism. Acetate kinase and phasin were 2 of the 19 proteins that were not detected in carbaryl-supported C3 cells, but detected in glucose-supported C3 cells. Down-production of phasin and polyhydroxyalkanoates in carbaryl-supported C3 cells suggests insufficient carbon sources and lower levels of primary metabolites to maintain an ordinary level of metabolism. Differential metabolomes (~196 identified polar metabolites) showed up-production of metabolites in pentose phosphate pathways and metabolisms of cysteine, cystine and some other amino acids, disaccharides and nicotinate, in contract to down-production of most of the other amino acids and hexoses. The proteomic and metabolomic analyses showed that carbaryl-supported C3 cells experienced strong toxic effects, oxidative stresses, DNA/RNA damages and carbon nutrient deficiency.

Comparative Protein and Metabolite Profiling Revealed a Metabolic Network in Response to Multiple Environmental Contaminants in Mycobacterium aromativorans JS19b1T

Mycobacterium aromativorans JS19b1(T) was isolated from a petroleum-contaminated site that was acclimated almost 100 years. In the present study, metabolism of several polycyclic aromatic hydrocarbons (PAHs) and structural analogues in JS19b1(T) was studied. The proteomic profiles were compared when JS19b1(T) was cultured in nutrient broth and glucose-, phenanthrene-, and phthalate-supplemented mineral media. Proteomic analysis showed notable characteristics of this species, for instance, the existence of enzymes for degradation of multiple classes of chemicals including biphenyl, phenanthrene, dibenzothiophene, and organophosphorus pesticides. Phenanthrene degradation enzymes were detected only in phenanthrene-fed cells, suggesting a very tight regulation of the enzymes. Detection of the other enzymes under various treatment conditions indicated that their regulation may be through very complex mechanisms. In comparison with common major metabolites, PAH transformations produced various types of potentially toxic intermediates, including epoxide, quinone, phenols, aldehydes, and phthalates. In a bioenergy production aspect, PAH transformation does not seem to provide substrates for glycolysis and pentose phosphate pathways. This study signifies the potential of protein profiling for studies of relatively uncharacterized bacteria for biodegradation of environmental pollutants.

Bioconcentration of Pirimiphos-methyl in Killifish (Oryzias latipes)

Killifish (Oryzias latipes) were exposed to an organophosphate pesticide, pirimiphos-methyl, in a flow-through system to determine the bioconcentration factor (BCF) following GLP (Good Laboratory Practice). This study was conducted at two different concentrations (1 and 10 μg/L) of 14 C-labeled pirimiphos-methyl for 28 days uptake and 14 days depuration according to the OECD 305 test guideline. The BCFss for total radioactive residues in whole fish were 1,251 and 1,277 for low and high concentrations, respectively. The BCFk based on the uptake and depuration rate constants were 1,200 for both low and high concentrations. During the depuration phase, the accumulated test substance was rapidly depurated from fish. Greater than 95% of the residue at steady-state was depurated after 2 days. Although the measured BCF values were high, pirimiphos-methyl could be evaluated as a low risk from bioaccumulation by aquatic organisms due to the short depuration period and low amount of bound residue (1.5%). We suggest that in evaluating bioaccumulation, not only the BCF should be considered, but also depuration time and bound residue in aquatic organisms give an indication of the potential environmental risks.