Metabolic Diversity in Bacterial Degradation of Aromatic Compounds

2007 ◽  
Vol 11 (3) ◽  
pp. 252-279 ◽  
Author(s):  
Prashant S. Phale ◽  
Aditya Basu ◽  
Prabin D. Majhi ◽  
Jaigeeth Deveryshetty ◽  
C. Vamsee-Krishna ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Bacterial Degradation ◽  
Metabolic Diversity

scholarly journals Bacterial Conversion of Hydroxylamino Aromatic Compounds by both Lyase and Mutase Enzymes Involves Intramolecular Transfer of Hydroxyl Groups

2003 ◽  
Vol 69 (5) ◽  
pp. 2786-2793 ◽  
Author(s):  
Lloyd J. Nadeau ◽  
Zhongqi He ◽  
Jim C. Spain
Keyword(s):  
Aromatic Compounds ◽  
Ralstonia Eutropha ◽  
Transfer Mechanism ◽  
Bacterial Degradation ◽  
Hydroxyl Group ◽  
Hydroxyl Groups ◽  
Reaction Products ◽  
Comamonas Acidovorans ◽  
Label Incorporation ◽  
Intramolecular Transfer

ABSTRACT Hydroxylamino aromatic compounds are converted to either the corresponding aminophenols or protocatechuate during the bacterial degradation of nitroaromatic compounds. The origin of the hydroxyl group of the products could be the substrate itself (intramolecular transfer mechanism) or the solvent water (intermolecular transfer mechanism). The conversion of hydroxylaminobenzene to 2-aminophenol catalyzed by a mutase from Pseudomonas pseudoalcaligenes JS45 proceeds by an intramolecular hydroxyl transfer. The conversions of hydroxylaminobenzene to 2- and 4-aminophenol by a mutase from Ralstonia eutropha JMP134 and to 4-hydroxylaminobenzoate to protocatechuate by a lyase from Comamonas acidovorans NBA-10 and Pseudomonas sp. strain 4NT were proposed, but not experimentally proved, to proceed by the intermolecular transfer mechanism. GC-MS analysis of the reaction products formed in H2 18O did not indicate any 18O-label incorporation during the conversion of hydroxylaminobenzene to 2- and 4-aminophenols catalyzed by the mutase from R. eutropha JMP134. During the conversion of 4-hydroxylaminobenzoate catalyzed by the hydroxylaminolyase from Pseudomonas sp. strain 4NT, only one of the two hydroxyl groups in the product, protocatechuate, was 18O labeled. The other hydroxyl group in the product must have come from the substrate. The mutase in strain JS45 converted 4-hydroxylaminobenzoate to 4-amino-3-hydroxybenzoate, and the lyase in Pseudomonas strain 4NT converted hydroxylaminobenzene to aniline and 2-aminophenol but not to catechol. The results indicate that all three types of enzyme-catalyzed rearrangements of hydroxylamino aromatic compounds proceed via intramolecular transfer of hydroxyl groups.

scholarly journals Epoxy Coenzyme A Thioester Pathways for Degradation of Aromatic Compounds

2012 ◽  
Vol 78 (15) ◽  
pp. 5043-5051 ◽  
Author(s):  
Wael Ismail ◽  
Johannes Gescher
Keyword(s):  
Aromatic Ring ◽  
Aromatic Compounds ◽  
Coenzyme A ◽  
Environmental Pollutants ◽  
Bacterial Degradation ◽  
Ring Cleavage ◽  
The Novel ◽  
Energy Consuming ◽  
Coa Thioesters ◽  
Hydrolytic Mechanism

ABSTRACTAromatic compounds (biogenic and anthropogenic) are abundant in the biosphere. Some of them are well-known environmental pollutants. Although the aromatic nucleus is relatively recalcitrant, microorganisms have developed various catabolic routes that enable complete biodegradation of aromatic compounds. The adopted degradation pathways depend on the availability of oxygen. Under oxic conditions, microorganisms utilize oxygen as a cosubstrate to activate and cleave the aromatic ring. In contrast, under anoxic conditions, the aromatic compounds are transformed to coenzyme A (CoA) thioesters followed by energy-consuming reduction of the ring. Eventually, the dearomatized ring is opened via a hydrolytic mechanism. Recently, novel catabolic pathways for the aerobic degradation of aromatic compounds were elucidated that differ significantly from the established catabolic routes. The new pathways were investigated in detail for the aerobic bacterial degradation of benzoate and phenylacetate. In both cases, the pathway is initiated by transforming the substrate to a CoA thioester and all the intermediates are bound by CoA. The subsequent reactions involve epoxidation of the aromatic ring followed by hydrolytic ring cleavage. Here we discuss the novel pathways, with a particular focus on their unique features and occurrence as well as ecological significance.

scholarly journals Bacterial Degradation of Aromatic Compounds

2009 ◽  
Vol 6 (1) ◽  
pp. 278-309 ◽  
Author(s):  
Jong-Su Seo ◽  
Young-Soo Keum ◽  
Qing Li
Keyword(s):  
Aromatic Compounds ◽  
Bacterial Degradation

scholarly journals Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds

2020 ◽  
Author(s):  
Masaya Fujita ◽  
Taichi Sakumoto ◽  
Kenta Tanatani ◽  
Hong Yang Yu ◽  
Kosuke Mori ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Aromatic Compounds ◽  
Iron Uptake ◽  
Iron Acquisition ◽  
Essential Element ◽  
Acquisition System ◽  
Bacterial Degradation ◽  
Iron Acquisition System ◽  
Iron Transporter ◽  
Outer Membrane Transporters

AbstractIron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae comprises various degraders of recalcitrant aromatic compounds; however, little is known about their iron acquisition system. Here, we investigated the iron acquisition system in a model bacterium capable of degrading lignin-derived aromatics, Sphingobium sp. strain SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, and tonB2 (SLG_34550), one of the six tonB comprising the Ton complex which enables TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB (SLG_36840) played an important role in iron uptake across the inner membrane. The promoter activities of most of the iron uptake genes were induced under iron-limited conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake regulator, Fur. Although feoB, among all the iron uptake genes identified is highly conserved in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation of the iron acquisition system promises better understanding of the bacterial degradation mechanisms of aromatic compounds.

scholarly journals Function of Coenzyme F420 in Aerobic Catabolism of 2,4,6-Trinitrophenol and 2,4-Dinitrophenol by Nocardioides simplex FJ2-1A

1999 ◽  
Vol 181 (9) ◽  
pp. 2669-2674 ◽  
Author(s):  
Sybille Ebert ◽  
Paul-Gerhard Rieger ◽  
Hans-Joachim Knackmuss
Keyword(s):  
Aromatic Compounds ◽  
Enzyme System ◽  
Picric Acid ◽  
Methanobacterium Thermoautotrophicum ◽  
Bacterial Degradation ◽  
Coenzyme F420 ◽  
Terminal Sequence ◽  
Aromatic System ◽  
Two Component ◽  
Protein Components

ABSTRACT 2,4,6-Trinitrophenol (picric acid) and 2,4-dinitrophenol were readily biodegraded by the strain Nocardioides simplexFJ2-1A. Aerobic bacterial degradation of these π-electron-deficient aromatic compounds is initiated by hydrogenation at the aromatic ring. A two-component enzyme system was identified which catalyzes hydride transfer to picric acid and 2,4-dinitrophenol. Enzymatic activity was dependent on NADPH and coenzyme F420. The latter could be replaced by an authentic preparation of coenzyme F420 fromMethanobacterium thermoautotrophicum. One of the protein components functions as a NADPH-dependent F420 reductase. A second component is a hydride transferase which transfers hydride from reduced coenzyme F420 to the aromatic system of the nitrophenols. The N-terminal sequence of the F420 reductase showed high homology with an F420-dependent NADP reductase found in archaea. In contrast, no N-terminal similarity to any known protein was found for the hydride-transferring enzyme.

Prerequisites for a bacterial degradation of N-,S, and O-heterocyclic, aromatic compounds

1988 ◽  
pp. 755-757
Author(s):  
J. R. Andreesen ◽  
M. Nagel ◽  
I. Siegmund ◽  
K. König ◽  
W. Freudenberg
Keyword(s):  
Aromatic Compounds ◽  
Bacterial Degradation

scholarly journals Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

2020 ◽  
Author(s):  
Ryota Moriuchi ◽  
Hideo Dohra ◽  
Yu Kanesaki ◽  
Naoto Ogawa
Keyword(s):  
Aromatic Compounds ◽  
Differential Expression Analysis ◽  
Agar Plate ◽  
Enrichment Analysis ◽  
Cupriavidus Necator ◽  
Major Facilitator Superfamily ◽  
Bacterial Degradation ◽  
Genes Encoding ◽  
Chlorinated Aromatic Compounds ◽  
Major Facilitator

Abstract BackgroundAromatic compounds derived from human activities are often released into the environment. Many of them, especially halogenated aromatics, are persistent in nature and pose threats to organisms. Therefore, the microbial degradation of these compounds has been studied intensively. Our laboratory has studied the expression of genes in Cupriavidus necator NH9 involved in the degradation of 3-chlorobenzoate (3-CB), a model compound for studies on bacterial degradation of chlorinated aromatic compounds. In this study aimed at exploring how this bacterium has adapted to the utilization of chlorinated aromatic compounds, we performed RNA-seq analysis of NH9 cells cultured with 3-CB, benzoate (BA), or citric acid (CA). The purpose of these analyses was to identify differentially expressed genes encoding products with various biological functions involved in the degradation of 3-CB and BA.ResultsDifferential expression analysis confirmed strong induction of genes encoding enzymes in degradation pathways of 3-CB and BA, including benABCD (more than 256-fold compared with CA) encoding benzoate 1,2-dioxygenase involved in initial hydroxylation of both 3-CB and BA, and cbnABCD (more than 200-fold compared with BA and CA) encoding enzymes of chlorocatechol ortho-cleavage pathway. Four genes encoding major facilitator superfamily transporters were specifically induced by 3-CB or BA, and one cluster of genes encoding components of the ATP-binding cassette transporter system was significantly induced by 3-CB. Stress response genes encoding chaperones, proteases, the phosphate transporter PstBACS, and superoxide oxidase were upregulated in response to 3-CB and/or BA. Gene Ontology enrichment analysis revealed that genes encoding dioxygenases were upregulated by both 3-CB and BA. Intriguingly, the “cell motility,” “signal transduction,” and “chemotaxis” terms were significantly upregulated by BA compared with 3-CB. Consistent with this, in semi-solid agar plate assays, NH9 cells showed stronger chemotaxis to BA than to 3-CB.ConclusionsOur results showed that the chemotaxis behavior of NH9 differs between 3-CB and BA. We inferred that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike its analogous aromatic compound BA, in nature.

scholarly journals Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

2020 ◽  
Author(s):  
Ryota Moriuchi ◽  
Hideo Dohra ◽  
Yu Kanesaki ◽  
Naoto Ogawa
Keyword(s):  
Aromatic Compounds ◽  
Differential Expression Analysis ◽  
Agar Plate ◽  
Enrichment Analysis ◽  
Cupriavidus Necator ◽  
Major Facilitator Superfamily ◽  
Bacterial Degradation ◽  
Genes Encoding ◽  
Chlorinated Aromatic Compounds ◽  
Major Facilitator

Abstract Background Aromatic compounds derived from human activities are often released into the environment. Many of them, especially halogenated aromatics, are persistent in nature and pose threats to organisms. Therefore, the microbial degradation of these compounds has been studied intensively. Our laboratory has studied the expression of genes in Cupriavidus necator NH9 involved in the degradation of 3-chlorobenzoate (3-CB), a model compound for studies on bacterial degradation of chlorinated aromatic compounds. In this study aimed at exploring how this bacterium has adapted to the utilization of chlorinated aromatic compounds, we performed RNA-seq analysis of NH9 cells cultured with 3-CB, benzoate (BA), or citric acid (CA). The purpose of these analyses was to identify differentially expressed genes encoding products with various biological functions involved in the degradation of 3-CB and BA. Results Differential expression analysis confirmed strong induction of genes encoding enzymes in degradation pathways of 3-CB and BA, including benABCD (more than 256-fold compared with CA) encoding benzoate 1,2-dioxygenase involved in initial hydroxylation of both 3-CB and BA, and cbnABCD (more than 200-fold compared with BA and CA) encoding enzymes of chlorocatechol ortho -cleavage pathway. Four genes encoding major facilitator superfamily transporters were specifically induced by 3-CB or BA, and one cluster of genes encoding components of the ATP-binding cassette transporter system was significantly induced by 3-CB. Stress response genes encoding chaperones, proteases, the phosphate transporter PstBACS, and superoxide oxidase were upregulated in response to 3-CB and/or BA. Gene Ontology enrichment analysis revealed that genes encoding dioxygenases were upregulated by both 3-CB and BA. Intriguingly, the “cell motility,” “signal transduction,” and “chemotaxis” terms were significantly upregulated by BA compared with 3-CB. Consistent with this, in semi-solid agar plate assays, NH9 cells showed stronger chemotaxis to BA than to 3-CB. Conclusions Our results showed that the chemotaxis behavior of NH9 differs between 3-CB and BA. We inferred that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike its analogous aromatic compound BA, in nature.

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