scholarly journals A New ICEclc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716

2021 ◽  
Vol 9 (12) ◽  
pp. 2462
Author(s):  
Jun Hirose ◽  
Takahito Watanabe ◽  
Taiki Futagami ◽  
Hidehiko Fujihara ◽  
Nobutada Kimura ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Variable Region ◽  
Pseudomonas Stutzeri ◽  
Intermediate Form ◽  
Integrative And Conjugative Elements ◽  
Bph Genes ◽  
Catabolic Genes ◽  
Degrading Bacteria ◽  
Genetic Features ◽  
Conserved Core

Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation o-f aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family carrying biphenyl catabolic bph genes and salicylic acid catabolic sal genes from the PCB-degrading strain Pseudomonas stutzeri KF716. The 117-kb ICEbph-salKF716 contains common core regions exhibiting homology with those of degradative ICEclc from P. knackmussii B13 and ICEXTD from Azoarcus sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from P. putida B6-2, P, alcaliphila JAB1, P. stutzeri AN10, and P. stutzeri 2A20 had highly conserved core regions with those of ICEbph-salKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICEbph-salKF716 was transferred from P. stutzeri KF716 to P. aeruginosa PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICEbph-salKF716 compared to other catabolic ICEs.

scholarly journals Novel Pathway for the Degradation of 2-Chloro-4-Nitrobenzoic Acid by Acinetobacter sp. Strain RKJ12

2011 ◽  
Vol 77 (18) ◽  
pp. 6606-6613 ◽  
Author(s):  
Dhan Prakash ◽  
Ravi Kumar ◽  
R. K. Jain ◽  
B. N. Tiwary
Keyword(s):  
Salicylic Acid ◽  
Tricarboxylic Acid Cycle ◽  
Sole Source ◽  
Degradation Pathway ◽  
Ring Cleavage ◽  
Muconic Acid ◽  
Content Type ◽  
Nitrobenzoic Acid ◽  
Catabolic Genes ◽  
Catechol 1,2 Dioxygenase

ABSTRACTThe organismAcinetobactersp. RKJ12 is capable of utilizing 2-chloro-4-nitrobenzoic acid (2C4NBA) as a sole source of carbon, nitrogen, and energy. In the degradation of 2C4NBA by strain RKJ12, various metabolites were isolated and identified by a combination of chromatographic, spectroscopic, and enzymatic activities, revealing a novel assimilation pathway involving both oxidative and reductive catabolic mechanisms. The metabolism of 2C4NBA was initiated by oxidativeorthodehalogenation, leading to the formation of 2-hydroxy-4-nitrobenzoic acid (2H4NBA), which subsequently was metabolized into 2,4-dihydroxybenzoic acid (2,4-DHBA) by a mono-oxygenase with the concomitant release of chloride and nitrite ions. Stoichiometric analysis indicated the consumption of 1 mol O2per conversion of 2C4NBA to 2,4-DHBA, ruling out the possibility of two oxidative reactions. Experiments with labeled H218O and18O2indicated the involvement of mono-oxygenase-catalyzed initial hydrolytic dechlorination and oxidative denitration mechanisms. The further degradation of 2,4-DHBA then proceeds via reductive dehydroxylation involving the formation of salicylic acid. In the lower pathway, the organism transformed salicylic acid into catechol, which was mineralized by theorthoring cleavage catechol-1,2-dioxygenase tocis, cis-muconic acid, ultimately forming tricarboxylic acid cycle intermediates. Furthermore, the studies carried out on a 2C4NBA−derivative and a 2C4NBA+transconjugant demonstrated that the catabolic genes for the 2C4NBA degradation pathway possibly reside on the ∼55-kb transmissible plasmid present in RKJ12.

Impact of nanoparticles on transcriptional regulation of catabolic genes of petroleum hydrocarbon-degrading bacteria in contaminated soil microcosms

2018 ◽  
Vol 59 (2) ◽  
pp. 166-180
Author(s):  
Wael S. El-Sayed ◽  
Yasser Elbahloul ◽  
Mohamed E. Saad ◽  
Ahmed M. Hanafy ◽  
Abdelrahman H. Hegazi ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Contaminated Soil ◽  
Petroleum Hydrocarbon ◽  
Soil Microcosms ◽  
Catabolic Genes ◽  
Degrading Bacteria

scholarly journals Eksplorasi Bakteri Indigen Pada Pembenihan Ikan Lele Dumbo (Clarias sp.) Sistem Resirkulasi Tertutup [Exploration Of Indigen Bacteria From Catfish (Clarias sp.) Breeding On Closed Resirculation System ]

2019 ◽  
Vol 4 (2) ◽  
pp. 193
Author(s):  
Prayogo, Boedi Setya Rahardja, Abdul Manan
Keyword(s):  
Organic Matter ◽  
Organic Materials ◽  
Pseudomonas Stutzeri ◽  
Bacterial Strains ◽  
Isolation And Identification ◽  
Biological Filtration ◽  
Degrading Bacteria ◽  
Recirculation System ◽  
Pseudomonas Pseudomallei

Abstract The efforts of the catfish hatchery fish are generally confined to the central areas of hatchery that has abundant water resources. Solving the problem of limited water, appears a catfish hatchery system with a closed recirculation system. In such systems the process of biological filtration is the most important thing. It shows the handling of organic materials by utilizing the degrading bacteria is the key to successful management of the system. Thus necessary to be studied the role of bacteria degrading organic matter indigen (local bacteria) in the closed hatchery recirculation system of catfish. This study aimed to obtain bacterial strains degrading bacteria indigen as organic materials are very useful in improving water quality in the closed hatchery recirculation system of catfish and knowing the methods to the use of bacteria indigen as degrading organic matter. The method used in this study was designed based on the stages of research carried out in accordance with the objectives to be achieved. The results of the isolation and identification to the species level showed Pseudomonas stutzeri and Pseudomonas pseudomallei obtain the greatest value for hydrolysis index representing each trait protease, lipase and amylase. Bioremediation effectiveness test in vitro showed effective results in the treatment using consortia of bacteria inoculant. Consortia of bacteria inoculant effective in improving the growth rate and survival rate (SR) in the closed hatchery recirculation system of catfish.

scholarly journals Activation and Inactivation of Pseudomonas stutzeriMethylbenzene Catabolism Pathways Mediated by a Transposable Element

1999 ◽  
Vol 65 (5) ◽  
pp. 1876-1882 ◽  
Author(s):  
Fabrizio Bolognese ◽  
Cinzia di Lecce ◽  
Enrica Galli ◽  
Paola Barbieri
Keyword(s):  
Transposable Element ◽  
Type Strain ◽  
Insertion Sequence ◽  
Wild Type Strain ◽  
Pseudomonas Stutzeri ◽  
Inverted Repeats ◽  
Wild Type ◽  
Catabolic Pathway ◽  
Catabolic Genes ◽  
Target Dna

ABSTRACT The arrangement of the genes involved in o-xylene,m-xylene, and p-xylene catabolism was investigated in three Pseudomonas stutzeri strains: the wild-type strain OX1, which is able to grow on o-xylene but not on the meta and para isomers; the mutant M1, which grows on m-xylene and p-xylene but is unable to utilize the ortho isomer; and the revertant R1, which can utilize all the three isomers of xylene. A 3-kb insertion sequence (IS) termed ISPs1, which inactivates them-xylene and p-xylene catabolic pathway inP. stutzeri OX1 and the o-xylene catabolic genes in P. stutzeri M1, was detected. No IS was detected in the corresponding catabolic regions of the P. stutzeri R1 genome. ISPs1 is present in several copies in the genomes of the three strains. It is flanked by 24-bp imperfect inverted repeats, causes the direct duplication of 8 bp in the target DNA, and seems to be related to the ISL3 family.

scholarly journals Cross-Regulation of Biphenyl- and Salicylate-Catabolic Genes by Two Regulatory Systems in Pseudomonas pseudoalcaligenes KF707

2006 ◽  
Vol 188 (13) ◽  
pp. 4690-4697 ◽  
Author(s):  
Hidehiko Fujihara ◽  
Hideyuki Yoshida ◽  
Tetsuya Matsunaga ◽  
Masatoshi Goto ◽  
Kensuke Furukawa
Keyword(s):  
Gene Cluster ◽  
Coenzyme A ◽  
Regulatory Gene ◽  
Pseudomonas Pseudoalcaligenes ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Regulatory Systems ◽  
Catabolic Genes ◽  
Degrading Bacteria ◽  
Regulatory Model

ABSTRACT Pseudomonas pseudoalcaligenes KF707 grows on biphenyl and salicylate as sole sources of carbon. The biphenyl-catabolic (bph) genes are organized as bphR1A1A2(orf3)A3A4BCX0X1X2X3D, encoding the enzymes for conversion of biphenyl to acetyl coenzyme A. In this study, the salicylate-catabolic (sal) gene cluster encoding the enzymes for conversion of salicylate to acetyl coenzyme A were identified 6.6-kb downstream of the bph gene cluster along with a second regulatory gene, bphR2. Both the bph and sal genes were cross-regulated positively and/or negatively by the two regulatory proteins, BphR1 and BphR2, in the presence or absence of the effectors. The BphR2 binding sequence exhibits homology with the NahR binding sequences in various naphthalene-degrading bacteria. Based on previous studies and the present study we propose a new regulatory model for biphenyl and salicylate catabolism in strain KF707.

scholarly journals Products from the Incomplete Metabolism of Pyrene by Polycyclic Aromatic Hydrocarbon-Degrading Bacteria

2000 ◽  
Vol 66 (5) ◽  
pp. 1917-1922 ◽  
Author(s):  
Chikoma Kazunga ◽  
Michael D. Aitken
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Pseudomonas Stutzeri ◽  
Minor Effect ◽  
Bacterial Strains ◽  
Phenanthrene Degradation ◽  
Degrading Bacteria ◽  
Subsequent Degradation ◽  
Polycyclic Aromatic ◽  
A Minor

ABSTRACT Pyrene is a regulated pollutant at sites contaminated with polycyclic aromatic hydrocarbons (PAH). It is mineralized by some bacteria but is also transformed to nonmineral products by a variety of other PAH-degrading bacteria. We examined the formation of such products by four bacterial strains and identified and further characterized the most apparently significant of these metabolites.Pseudomonas stutzeri strain P16 and Bacillus cereus strain P21 transformed pyrene primarily tocis-4,5-dihydro-4,5-dihydroxypyrene (PYRdHD), the first intermediate in the known pathway for aerobic bacterial mineralization of pyrene. Sphingomonas yanoikuyae strain R1 transformed pyrene to PYRdHD and pyrene-4,5-dione (PYRQ). Both strain R1 and Pseudomonas saccharophila strain P15 transform PYRdHD to PYRQ nearly stoichiometrically, suggesting that PYRQ is formed by oxidation of PYRdHD to 4,5-dihydroxypyrene and subsequent autoxidation of this metabolite. A pyrene-mineralizing organism,Mycobacterium strain PYR-1, also transforms PYRdHD to PYRQ at high initial concentrations of PYRdHD. However, strain PYR-1 is able to use both PYRdHD and PYRQ as growth substrates. PYRdHD strongly inhibited phenanthrene degradation by strains P15 and R1 but had only a minor effect on strains P16 and P21. At their aqueous saturation concentrations, both PYRdHD and PYRQ severely inhibited benzo[a]pyrene mineralization by strains P15 and R1. Collectively, these findings suggest that products derived from pyrene transformation have the potential to accumulate in PAH-contaminated systems and that such products can significantly influence the removal of other PAH. However, these products may be susceptible to subsequent degradation by organisms able to metabolize pyrene more extensively if such organisms are present in the system.

scholarly journals Pseudomonas putida Strain PCL1444, Selected for Efficient Root Colonization and Naphthalene Degradation, Effectively Utilizes Root Exudate Components

2002 ◽  
Vol 15 (7) ◽  
pp. 734-741 ◽  
Author(s):  
Irene Kuiper ◽  
Lev V. Kravchenko ◽  
Guido V. Bloemberg ◽  
Ben J. J. Lugtenberg
Keyword(s):  
Salicylic Acid ◽  
Succinic Acid ◽  
Pseudomonas Putida ◽  
Root Exudate ◽  
Carbon Sources ◽  
Degradation Pathway ◽  
Root Tip ◽  
Logarithmic Phase ◽  
Naphthalene Degradation ◽  
Catabolic Genes

Previously, we have described the selection of a plant-bacterium pair that is efficient in rhizoremediating naphthalene pollution in microcosm studies. After repeated selection for efficient root tip colonization upon inoculation of seeds of grass cv. Barmultra and for stable and efficient growth on naphthalene, Pseudomonas putida PCL1444 was selected as the most efficient colonizer of Barmultra roots. Here, we report the analysis of Barmultra root exudate composition and our subsequent tests of the growth rate of the bacterium and of the expression of the naphthalene degradation genes on individual exudate components. High performance liquid chromatography analysis of the organic acid and sugar root-exudate components revealed that glucose and fructose are the most abundant sugars, whereas succinic acid and citric acid are the most abundant organic acids. Tn5luxAB mutants of PCL1444 impaired in naphthalene degradation appeared to be impaired in genes homologous to genes of the upper naphthalene degradation pathway present in various Pseudomonas strains and to genes of the lower pathway genes for naphthalene degradation in P. stutzeri. Highest expression for both pathways involved in naphthalene degradation during growth in minimal medium with the carbon source to be tested was observed at the start of the logarithmic phase. Naphthalene did not induce the upper pathway, but a different pattern of expression was observed in the lower pathway reporter, probably due to the conversion of naphthalene to salicylic acid. Salicylic acid, which is described as an intermediate of the naphthalene degradation pathway in many Pseudomonas strains, did induce both pathways, resulting in an up to sixfold higher expression level at the start of the logarithmic phase. When expression levels during growth on the different carbon sources present in root exudate were compared, highest expression was observed on the two major root exudate components, glucose and succinic acid. These results show an excellent correlation between successful naphthalene rhizoremediation by the Barmultra-P. putida PCL1444 pair and both efficient utilization of the major exudate components for growth and high transcription of the naphthalene catabolic genes on the major exudate components. Therefore, we hypothesize that efficient root colonizing and naphthalene degradation is the result of the applied colonization enrichment procedure.

scholarly journals Construction of Chimeric Catechol 2,3-Dioxygenase Exhibiting Improved Activity against the Suicide Inhibitor 4-Methylcatechol

2004 ◽  
Vol 70 (3) ◽  
pp. 1804-1810 ◽  
Author(s):  
Akiko Okuta ◽  
Kouhei Ohnishi ◽  
Shigeaki Harayama
Keyword(s):  
Ascorbic Acid ◽  
Pseudomonas Putida ◽  
Gene Sequence ◽  
Mixed Cultures ◽  
Enzyme Inactivation ◽  
Host Cells ◽  
Ring Cleavage ◽  
Gene Sequences ◽  
Catabolic Genes ◽  
Degrading Bacteria

ABSTRACT Catechol 2,3-dioxygenase (C23O; EC 1.3.11.2), exemplified by XylE and NahH, catalyzes the ring cleavage of catechol and some substituted catechols. C23O is inactivated at an appreciable rate during the ring cleavage of 4-methylcatechol due to the oxidation of the Fe(II) cofactor to Fe(III). In this study, a C23O exhibiting improved activity against 4-methylcatechol was isolated. To isolate this C23O, diverse C23O gene sequences were PCR amplified from DNA which had been isolated from mixed cultures of phenol-degrading bacteria and subcloned in the middle of a known C23O gene sequence (xylE or nahH) to construct a library of chimeric C23O genes. These chimeric C23O genes were then introduced into Pseudomonas putida possessing some of the toluene catabolic genes (xylXYZLGFJQKJI). When a C23O gene (e.g., xylE) is introduced into this strain, the transformants cannot generally grow on p-toluate because 4-methylcatechol, a metabolite of p-toluate, is a substrate as well as a suicide inhibitor of C23O. However, a transformant of this strain capable of growing on p-toluate was isolated, and a chimeric C23O (named NY8) in this transformant was characterized. The rate of enzyme inactivation by 4-methylcatechol was lower in NY8 than in XylE. Furthermore, the rate of the reactivation of inactive C23O in a solution containing Fe(II) and ascorbic acid was higher in NY8 than in XylE. These properties of NY8 might allow the efficient metabolism of 4-methylcatechol and thus allow host cells to grow on p-toluate.

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