Biodegradation of p-xylene – A comparison for three Cold-active Pseudomonas strains

Abstract p-xylene is considered a recalcitrant compound despite the similar aromatic structure with BTE (Benzene, toluene, ethylbenzene). This study evaluated the biodegradation potential of p-xylene by three cold-active Pseudomonas strains (named Pseudomonas putida S2TR-01, Pseudomonas S2TR-20, and Pseudomonas S2TR-09). The catabolic genes (xylM, xylA and xylE) and their regulatory genes (xylR and xylS) were investigated for the p-xylene metabolism. The biodegradation results showed that only strain S2TR-09 was able to degrade 200 mg/L of p-xylene after 60 h at 15 °C. The gene expression study indicated that xylE (encoding catechol 2, 3-dioxygenase) represents the bottleneck for p-xylene biodegradation and lack of its expression leads to the accumulation of intermediates and inhibits biomass production as well as carbon recovery. The activity of xylene monooxygenase and catechol 2,3 dioxygenase was significantly high in P. azotoformans S2TR-09 (0.5 and 0.08 U/mg) in the presence of p-xylene. The expression of ring cleavage enzyme, its encoding genes (xylE), and its activator (xylS) enabled to link the differences in p-xylene metabolism and can be used as a novel biomarker for efficient p-xylene biodegradation in contaminated sites.

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Genetic Analysis of Dioxin Dioxygenase ofSphingomonas sp. Strain RW1: Catabolic Genes Dispersed on the Genome

Journal of Bacteriology ◽

10.1128/jb.180.15.3954-3966.1998 ◽

1998 ◽

Vol 180 (15) ◽

pp. 3954-3966 ◽

Cited By ~ 108

Author(s):

Jean Armengaud ◽

Birgitta Happe ◽

Kenneth N. Timmis

Keyword(s):

Supply System ◽

Ring Cleavage ◽

Gene Encoding ◽

Genetic Organization ◽

Catabolic Genes ◽

Genes Encoding ◽

Subsequent Step ◽

Cleavage Enzyme ◽

Angular Dioxygenation ◽

Class Iib

ABSTRACT The dioxin dioxygenase of Sphingomonas sp. strain RW1 activates dibenzo-p-dioxin and dibenzofuran for further metabolism by introducing two atoms of oxygen at a pair of vicinal carbon atoms, one of which is involved in one of the bridges between the two aromatic rings, i.e., an angular dioxygenation. ThedxnA1 and dxnA2 cistrons encoding this dioxygenase have been cloned and shown to be located just upstream of a hydrolase gene which specifies an enzyme involved in the subsequent step of the dibenzofuran biodegradative pathway. Genes encoding the electron supply system of the dioxygenase are not clustered with the dioxygenase gene but rather are located on two other distinct and separate genome segments. Moreover, whereas expression ofdxnA1A2 is modulated according to the available carbon source, expression of the dbfB gene encoding the ring cleavage enzyme of the dibenzofuran pathway, which is located in the neighborhood of dxnA1A2 but oriented in the opposite direction, is constitutive. The scattering of genes for the component proteins of dioxin dioxygenase system around the genome ofSphingomonas sp. strain RW1, and the differential expression of dioxin pathway genes, is unusual and contrasts with the typical genetic organization of catabolic pathways where component cistrons tend to be clustered in multicistronic transcriptional units. The sequences of the α and β subunits of the dioxin dioxygenase exhibit only weak similarity to other three component dioxygenases, but some motifs such as the Fe(II) binding site and the [2Fe-2S] cluster ligands are conserved. Dioxin dioxygenase activity in Escherichia coli cells containing the cloned dxnA1A2 gene was achieved only through coexpression of the cognate electron supply system from RW1. Under these conditions, exclusively angular dioxygenation of dibenzofuran and dibenzo-p-dioxin was obtained. The dioxin dioxygenase was not active in E. colicells coexpressing a class IIB electron supply system. In the course of the isolation of the dxnA1 and dxnA2 cistrons, a number of other catabolic genes dispersed over different genome segments were identified, which may indicate greater catabolic potential than was previously suspected. This finding is consistent with the catabolic versatility of members of the genusSphingomonas, which is becoming increasingly evident, and may indicate a less well evolved and regulated but more dynamic genetic organization in this organism than is the case for better-studied pathways in organisms such as Pseudomonas species.

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A Gene Expression Study of the Activities of Aromatic Ring-Cleavage Dioxygenases in Mycobacterium gilvum PYR-GCK to Changes in Salinity and pH during Pyrene Degradation

PLoS ONE ◽

10.1371/journal.pone.0058066 ◽

2013 ◽

Vol 8 (2) ◽

pp. e58066 ◽

Cited By ~ 31

Author(s):

Abimbola Comfort Badejo ◽

Adegoke Olugboyega Badejo ◽

Kyung Hoon Shin ◽

Young Gyu Chai

Keyword(s):

Gene Expression ◽

Aromatic Ring ◽

Ring Cleavage ◽

Gene Expression Study ◽

Expression Study ◽

Pyrene Degradation ◽

Aromatic Ring Cleavage

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Comparative gene expression study in WM164 melanoma cells treated with dimethylacrylshikonin.

10.1055/s-0037-1608069 ◽

2017 ◽

Author(s):

N Kretschmer ◽

A Deutsch ◽

B Rinner ◽

M Scheideler ◽

R Bauer

Keyword(s):

Gene Expression ◽

Melanoma Cells ◽

Gene Expression Study ◽

Expression Study

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A gene expression study of the glutamate-nitric oxide pathway in schizophrenia

10.26226/morressier.5b681761b56e9b005965c319 ◽

2018 ◽

Author(s):

Makoto Kinoshita ◽

Florian Freudenberg ◽

Esin Candemir ◽

Sarah Kittel-Schneider

Keyword(s):

Gene Expression ◽

Nitric Oxide ◽

Gene Expression Study ◽

Expression Study ◽

Nitric Oxide Pathway

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Faculty Opinions recommendation of A gene expression study of normal and damaged cartilage in anteromedial gonarthrosis, a phenotype of osteoarthritis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718215615.793492102 ◽

2014 ◽

Author(s):

Ali Mobasheri

Keyword(s):

Gene Expression ◽

Gene Expression Study ◽

Expression Study

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Identification of Novel GH-Regulated Pathway of Lipid Metabolism in Adipose Tissue: A Gene Expression Study in Hypopituitary Men

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2010-2679 ◽

2011 ◽

Vol 96 (7) ◽

pp. E1188-E1196 ◽

Cited By ~ 20

Author(s):

Jing Ting Zhao ◽

Mark J. Cowley ◽

Paul Lee ◽

Vita Birzniece ◽

Warren Kaplan ◽

...

Keyword(s):

Gene Expression ◽

Adipose Tissue ◽

Lipid Metabolism ◽

Gene Expression Study ◽

Expression Study

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P.0900 The potential role of interferon signaling in migraine: a gene expression study

European Neuropsychopharmacology ◽

10.1016/j.euroneuro.2021.10.756 ◽

2021 ◽

Vol 53 ◽

pp. S661-S662

Author(s):

S. Kumar ◽

K. Gecse ◽

D. Baksa ◽

X. Gonda ◽

G. Bagdy ◽

...

Keyword(s):

Gene Expression ◽

Potential Role ◽

Gene Expression Study ◽

Interferon Signaling ◽

Expression Study

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Differential Roles of Three Different Upper Pathway Meta Ring Cleavage Product Hydrolases in the Degradation of Dibenzo- p -dioxin and Dibenzofuran by Sphingomonas wittichii RW1

Applied and Environmental Microbiology ◽

10.1128/aem.01067-21 ◽

2021 ◽

Author(s):

Thamer Y. Mutter ◽

Gerben J. Zylstra

Keyword(s):

Gene Knockout ◽

Sole Source ◽

Cleavage Product ◽

Ring Cleavage ◽

Catabolic Pathway ◽

Double Knockout ◽

Cleavage Enzyme ◽

Sphingomonas Wittichii ◽

Physiological Approach

Sphingomonas wittichii RW1 grows on the two related compounds dibenzofuran (DBF) and dibenzo- p -dioxin (DXN) as the sole source of carbon. Previous work by others (P.V. Bunz, R. Falchetto, and A.M. Cook. Biodegradation 4:171-8, 1993, doi: 10.1007/BF00695119) identified two upper pathway meta cleavage product hydrolases (DxnB1 and DxnB2) active on the DBF upper pathway metabolite 2-hydroxy-6-oxo-6-(2-hydroxyphenyl)-hexa-2,4-dienoate. We took a physiological approach to determine the role of these two enzymes in the degradation of DBF and DXN by RW1. Single knockouts of either plasmid located dbfB1 or chromosome located dbfB2 had no effect on RW1 growth on either DBF or DXN. However, a double knockout lost the ability to grow on DBF but still grew normally on DXN demonstrating that DbfB1 and DbfB2 are the only hydrolases involved in the DBF upper pathway. Using a transcriptomic-guided approach we identified a constitutively expressed third hydrolase encoded by the chromosomally located SWIT0910 gene. Knockout of SWIT0910 resulted in a strain that no longer grows on DXN but still grows normally on DBF. Thus the DbfB1 and DbfB2 hydrolases function in the DBF but not the DXN catabolic pathway and the SWIT0190 hydrolase functions in the DXN but not the DBF catabolic pathway. Importance S. wittichii RW1 is one of only a few strains known to grow on DXN as the sole course of carbon. Much of the work deciphering the related RW1 DXN and DBF catabolic pathways has involved genome gazing, transcriptomics, proteomics, heterologous expression, and enzyme purification and characterization. Very little research has utilized physiological techniques to precisely dissect the genes and enzymes involved in DBF and DXN degradation. Previous work by others identified and extensively characterized two RW1 upper pathway hydrolases. Our present work demonstrates that these two enzymes are involved in DBF but not DXN degradation. In addition, our work identified a third constitutively expressed hydrolase that is involved in DXN but not DBF degradation. Combined with our previous work, this means that the RW1 DXN upper pathway involves genes from three very different locations in the genome: an initial plasmid-encoded dioxygenase and a ring cleavage enzyme and hydrolase encoded on opposite sides of the chromosome.

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