Prashant S. Phale

Evidence for the involvement of multiple pathways in the biodegradation of 1- and 2-methylnaphthalene by Pseudomonas putida CSV86.

Pseudomonas putida CSV86, a soil bacterium, grows on 1- and 2-methylnaphthalene as the sole source of carbon and energy. In order to deduce the pathways for the biodegradation of 1- and 2-methylnaphthalene, metabolites were isolated from the spent medium and purified by thin layer chromatography. Emphasis has been placed on the structural characterisation of isolated intermediates by GC-MS, demonstration of enzyme activities in the cell free extracts and measurement of oxygen uptake by whole cells in the presence of various probable metabolic intermediates. The data obtained from such a study suggest the possibility of occurrence of multiple pathways in the degradation of 1- and 2-methylnaphthalene. We propose that, in one of the pathways, the aromatic ring adjacent to the one bearing the methyl moiety is oxidized leading to the formation of methylsalicylates and methylcatechols. In another pathway the methyl side chain is hydroxylated to-CH2OH which is further converted to-CHO and-COOH resulting in the formation of naphthoic acid as the end product. In addition to this, 2-hydroxymethylnaphthalene formed by the hydroxylation of the methyl group of 2-methylnaphthalene undergoes aromatic ring hydroxylation. The resultant dihydrodiol is further oxidised by a series of enzyme catalysed reactions to form 4-hydroxymethyl catechol as the end product of the pathway.

Preferential Utilization of Aromatic Compounds over Glucose by Pseudomonas putida CSV86

ABSTRACT Pseudomonas putida CSV86, a naphthalene-degrading organism, exhibited diauxic growth on aromatic compounds plus glucose, with utilization of aromatics in the first log phase and of glucose in the second log phase. Glucose supplementation did not suppress the activity of degrading enzymes, which were induced upon addition of aromatic compounds. The induction was inhibited by chloramphenicol, suggesting that de novo protein synthesis was essential. Cells showed cometabolism of aromatic compounds and organic acids; however, organic acids suppressed glucose utilization.

Metabolism of Carbaryl via 1,2-Dihydroxynaphthalene by Soil Isolates Pseudomonas sp. Strains C4, C5, and C6

ABSTRACT Pseudomonas sp. strains C4, C5, and C6 utilize carbaryl as the sole source of carbon and energy. Identification of 1-naphthol, salicylate, and gentisate in the spent media; whole-cell O2 uptake on 1-naphthol, 1,2-dihydroxynaphthalene, salicylaldehyde, salicylate, and gentisate; and detection of key enzymes, viz, carbaryl hydrolase, 1-naphthol hydroxylase, 1,2-dihydroxynaphthalene dioxygenase, and gentisate dioxygenase, in the cell extract suggest that carbaryl is metabolized via 1-naphthol, 1,2-dihydroxynaphthalene, and gentisate. Here, we demonstrate 1-naphthol hydroxylase and 1,2-dihydroxynaphthalene dioxygenase activities in the cell extracts of carbaryl-grown cells. 1-Naphthol hydroxylase is present in the membrane-free cytosolic fraction, requires NAD(P)H and flavin adenine dinucleotide, and has optimum activity in the pH range 7.5 to 8.0. Carbaryl-degrading enzymes are inducible, and maximum induction was observed with carbaryl. Based on these results, the proposed metabolic pathway is carbaryl → 1-naphthol → 1,2-dihydroxynaphthalene → salicylaldehyde → salicylate → gentisate → maleylpyruvate.

Bacterial degradation of phthalate isomers and their esters

Phthalate isomers and their esters are used heavily in various industries. Excess use and leaching from the product pose them as major pollutants. These chemicals are toxic, teratogenic, mutagenic and carcinogenic in nature. Various aspects like toxicity, diversity in the aerobic bacterial degradation, enzymes and genetic organization of the metabolic pathways from various bacterial strains are reviewed here. Degradation of these esters proceeds by the action of esterases to form phthalate isomers, which are converted to dihydroxylated intermediates by specific and inducible phthalate isomer dioxygenases. Metabolic pathways of phthalate isomers converge at 3,4-dihydroxybenzoic acid, which undergoes either ortho- or meta- ring cleavage and subsequently metabolized to the central carbon pathway intermediates. The genes involved in the degradation are arranged in operons present either on plasmid or chromosome or both, and induced by specific phthalate isomer. Understanding metabolic pathways, diversity and their genetic regulation may help in constructing bacterial strains through genetic engineering approach for effective bioremediation and environmental clean up.

A pathway for biodegradation of 1-naphthoic acid by Pseudomonas maltophilia CSV89

Pseudomonas maltophilia CSV89, a bacterium isolated from soil in our laboratory, grows on 1-naphthoic acid as the sole source of carbon and energy. To elucidate the pathway for degradation of 1-naphthoic acid, the metabolites were isolated from spent medium, purified by TLC, and characterized by gas chromatography-mass spectrometry. The involvement of various metabolites as intermediates in the pathway was established by demonstrating relevant enzyme activities in cell-free extracts, oxygen uptake and transformation of metabolites by the whole cells. The results obtained from such studies suggest that the degradation of 1-naphthoic acid is initiated by double hydroxylation of the aromatic ring adjacent to the one bearing the carboxyl group, resulting in the formation of 1,2-dihydroxy-8-carboxynaphthalene. The resultant diol was oxidized via 3-formyl salicylate, 2-hydroxyisophthalate, salicylate and catechol to TCA cycle intermediates.

Repression of the glucose-inducible outer- membrane protein OprB during utilization of aromatic compounds and organic acids in Pseudomonas putida CSV86

Pseudomonas putida CSV86 shows preferential utilization of aromatic compounds over glucose. Protein analysis and [¹⁴C]glucose-binding studies of the outer membrane fraction of cells grown on different carbon sources revealed a 40 kDa protein that was transcriptionally induced by glucose and repressed by aromatics and succinate. Based on 2D gel electrophoresis and liquid chromatography-tandem mass spectrometry analysis, the 40 kDa protein closely resembled the porin B of P. putida KT2440 and carbohydrate-selective porin OprB of various Pseudomonas strains. The purified native protein (i) was estimated to be a homotrimer of 125 kDa with a subunit molecular mass of 40 kDa, (ii) displayed heat modifiability of electrophoretic mobility, (iii) showed channel conductance of 166 pS in 1 M KCl, (iv) permeated various sugars (mono-, di- and tri-saccharides), organic acids, amino acids and aromatic compounds, and (v) harboured a glucose-specific and saturable binding site with a dissociation constant of 1.3 µM. These results identify the glucose-inducible outer-membrane protein of P. putida CSV86 as a carbohydrate-selective protein OprB. Besides modulation of intracellular glucose-metabolizing enzymes and specific glucose-binding periplasmic space protein, the repression of OprB by aromatics and organic acids, even in the presence of glucose, also contributes significantly to the strains ability to utilize aromatics and organic acids over glucose.

Modulation of Glucose Transport Causes Preferential Utilization of Aromatic Compounds in Pseudomonas putida CSV86

Pseudomonas putida CSV86 utilizes aromatic compounds in preference to glucose and coutilizes aromatics and organic acids. Protein analysis of cells grown on different carbon sources, either alone or in combination, revealed that a 43-kDa periplasmic-space protein was induced by glucose and repressed by aromatics and succinate. Two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry analysis identified this protein as closely resembling the sugar ABC transporter of Pseudomonas putida KT2440. A partially purified 43-kDa protein showed glucose binding activity and was specific for glucose. The results demonstrate that the aromatic- and organic acid-mediated repression of a periplasmic-space glucose binding protein and consequent inhibition of glucose transport are responsible for this strains ability to utilize aromatics and organic acids in preference to glucose.

Pseudomonas putida CSV86: A Candidate Genome for Genetic Bioaugmentation

Pseudomonas putida CSV86, a plasmid-free strain possessing capability to transfer the naphthalene degradation property, has been explored for its metabolic diversity through genome sequencing. The analysis of draft genome sequence of CSV86 (6.4 Mb) revealed the presence of genes involved in the degradation of naphthalene, salicylate, benzoate, benzylalcohol, p-hydroxybenzoate, phenylacetate and p-hydroxyphenylacetate on the chromosome thus ensuring the stability of the catabolic potential. Moreover, genes involved in the metabolism of phenylpropanoid and homogentisate, as well as heavy metal resistance, were additionally identified. Ability to grow on vanillin, veratraldehyde and ferulic acid, detection of inducible homogentisate dioxygenase and growth on aromatic compounds in the presence of heavy metals like copper, cadmium, cobalt and arsenic confirm in silico observations reflecting the metabolic versatility. In silico analysis revealed the arrangement of genes in the order: tRNAGly, integrase followed by nah operon, supporting earlier hypothesis of existence of a genomic island (GI) for naphthalene degradation. Deciphering the genomic architecture of CSV86 for aromatic degradation pathways and identification of elements responsible for horizontal gene transfer (HGT) suggests that genetic bioaugmentation strategies could be planned using CSV86 for effective bioremediation.

Metabolism and Preferential Utilization of Phenylacetic acid and 4-Hydroxyphenylacetic Acid in Pseudomonas putida CSV86

Metabolic pathways for phenylaceticacid (PA) and 4-hydroxyphenylacetic acid (4-HPA) from Pseudomonas putida CSV86 were elucidated. PA grown strain CSV86 cells showed higher oxygen-uptake on PA as compared to hydroxyphenylacetic acids. Detection of phenylacetyl-CoA ligase and absence of 4-hydroxyphenylacetic acid hydroxylase (4HPAH) and 3,4-dihydroxyphenylacetic acid-dioxygenase (3,4-DHPADO) activity supports this observation. 4-HPA grown cells showed oxygen-uptake on 4-HPA and 3,4-dihydroxyphenylacetic acid (3,4-DHPA) but showed significantly lower respiration rates on 2,5-dihydroxyphenylacetic acid and PA. Detection of 4HPAH and 3,4-DHPADO activities support the respiration data. Metabolic studies indicate that strain CSV86 metabolizes PA via phenylacetyl-CoA while 4-HPA via 3,4-DHPA pathway. Glucose grown cells showed lower activity of enzymes and respiration on PA, 4-HPA and 3,4-DHPA, suggesting that pathways are inducible. When grown on double carbon sources such as PA or 4-HPA plus glucose, CSV86 cells showed diauxic growth pattern with oxygen uptake on PA, 4-HPA and 3,4-DHPA in the first log-phase which was reduced during the second log-phase with increase in the respiration rate on glucose. This observation was supported by detection of high 4HPAH and 3,4-DHPADO activity in the first log-phase and glucose-6-phosphate dehydrogenase activity in the second log-phase. These results suggest that strain CSV86 utilizes PA and 4-HPA preferentially over glucose.

Genome Sequence of Naphthalene-Degrading Soil Bacterium Pseudomonas putida CSV86.

ABSTRACT Pseudomonas putida CSV86, a soil isolate, preferentially utilizes naphthalene over glucose as a source of carbon and energy. We present the draft genome sequence, which is 6.4 Mb in size; analysis suggests the chromosomal localization of genes coding for naphthalene utilization. The operons coding for glucose and other aromatic compounds might also be annotated in another study.