@article{2-s2.0-85149843765,

title = {Evaluation of the Defined Bacterial Consortium Efficacy in the Biodegradation of NSAIDs},

author = { A. Marchlewicz and U. Guzik and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85149843765&doi=10.3390%2fmolecules28052185&partnerID=40&md5=4092d66ed33e1bc7f11ea9018ced134c},

doi = {10.3390/molecules28052185},

issn = {14203049},

year  = {2023},

date = {2023-01-01},

journal = {Molecules},

volume = {28},

number = {5},

publisher = {MDPI},

abstract = {Due to the increasing pollution of wastewater with non-steroidal anti-inflammatory drugs, preparations need to be developed to decompose these drugs. This work aimed to develop a bacterial consortium with a defined composition and boundary conditions for the degradation of paracetamol and selected non-steroidal anti-inflammatory drugs (NSAIDs), including ibuprofen, naproxen, and diclofenac. The defined bacterial consortium consisted of Bacillus thuringiensis B1(2015b) and Pseudomonas moorei KB4 strains in a ratio of 1:2. During the tests, it was shown that the bacterial consortium worked in the pH range from 5.5 to 9 and temperatures of 15–35 °C, and its great advantage was its resistance to toxic compounds present in sewage, such as organic solvents, phenols, and metal ions. The degradation tests showed that, in the presence of the defined bacterial consortium in the sequencing batch reactor (SBR), drug degradation occurred at rates of 4.88, 10, 0.1, and 0.05 mg/day for ibuprofen, paracetamol, naproxen, and diclofenac, respectively. In addition, the presence of the tested strains was demonstrated during the experiment as well as after its completion. Therefore, the advantage of the described bacterial consortium is its resistance to the antagonistic effects of the activated sludge microbiome, which will enable it to be tested in real activated sludge conditions. © 2023 by the authors.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85144688398,

title = {Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens},

author = { D. Chlebek and T.M. Tame and A. Piński and J. Żur and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85144688398&doi=10.3390%2fijms232415561&partnerID=40&md5=8d122b0a287be7d39297e5d8632c6b68},

doi = {10.3390/ijms232415561},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {24},

publisher = {MDPI},

abstract = {Fungal phytopathogens are challenging to control due to their penetration into plant tissues. Therefore, plant-colonizing bacteria could serve as an excellent weapon in fighting fungal infections. In this study, we aim to determine the biocontrol potential of the new endophytic strain Serratia quinivorans KP32, isolated from the roots of Petroselinum crispum L.; identify the related mechanisms; and understand the basis of its antagonistic interaction with taxonomically diverse fungi at the molecular level. The KP32 strain presented biological activity against Rhizoctonia solani, Colletotrichum dematium, Fusarium avenaceum, and Sclerotinia sclerotiorum, and its ability to inhibit the growth of the phytopathogens was found to be mediated by a broad spectrum of biocontrol features, such as the production of a number of lytic enzymes (amylases; chitinases; and proteases), siderophores, volatile organic and inorganic compounds, salicylic acid, and N-acyl-homoserine lactones. The higher expression of chitinase (chiA) and genes involved in the biosynthesis of hydrogen cyanide (hcnC), enterobactin (entB), and acetoin (budA) in bacteria exposed to fungal filtrates confirmed that these factors could act in combination, leading to a synergistic inhibitory effect of the strain against phytopathogens. We also confirm the active movement, self-aggregation, exopolysaccharide production, and biofilm formation abilities of the KP32 strain, which are essential for effective plant colonization. Its biological activity and colonization potential indicate that KP32 holds tremendous potential for use as an active biopesticide and plant growth promoter. © 2022 by the authors.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85121668492,

title = {Analysis of the genome of the heavy metal resistant and hydrocarbon-degrading rhizospheric pseudomonas qingdaonensis zcr6 strain and assessment of its plant-growth-promoting traits},

author = { D. Chlebek and T. Płociniczak and S. Gobetti and A. Kumor and K.T. Hupert-Kocurek and M. Pacwa-Płociniczak},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121668492&doi=10.3390%2fijms23010214&partnerID=40&md5=db0b844c58764bf8192f1cb2aad87623},

doi = {10.3390/ijms23010214},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {1},

publisher = {MDPI},

abstract = {The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca3 (PO4 )2, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg−1 h−1 ). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5; 15; and 10 mM metal; respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85096339783,

title = {Genome mining and evaluation of the biocontrol potential of pseudomonas fluorescens brz63, a new endophyte of oilseed rape (Brassica napus l.) against fungal pathogens},

author = { D. Chlebek and A. Piński and J. Żur and J. Michalska and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096339783&doi=10.3390%2fijms21228740&partnerID=40&md5=87d4457488d36bc724971e34dcfdacb3},

doi = {10.3390/ijms21228740},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {22},

pages = {1-21},

publisher = {MDPI AG},

abstract = {Endophytic bacteria hold tremendous potential for use as biocontrol agents. Our study aimed to investigate the biocontrol activity of Pseudomonas fluorescens BRZ63, a new endophyte of oilseed rape (Brassica napus L.) against Rhizoctonia solani W70, Colletotrichum dematium K, Sclerotinia sclerotiorum K2291, and Fusarium avenaceum. In addition, features crucial for biocontrol, plant growth promotion, and colonization were assessed and linked with the genome sequences. The in vitro tests showed that BRZ63 significantly inhibited the mycelium growth of all tested pathogens and stimulated germination and growth of oilseed rape seedlings treated with fungal pathogens. The BRZ63 strain can benefit plants by producing biosurfactants, siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia as well as phosphate solubilization. The abilities of exopolysaccharide production, autoaggregation, and biofilm formation additionally underline its potential to plant colonization and hence biocontrol. The effective colonization properties of the BRZ63 strain were confirmed by microscopy observations of EGFP-expressing cells colonizing the root surface and epidermal cells of Arabidopsis thaliana Col-0. Genome mining identified many genes related to the biocontrol process, such as transporters, siderophores, and other secondary metabolites. All analyses revealed that the BRZ63 strain is an excellent endophytic candidate for biocontrol of various plant pathogens and plant growth promotion. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85087866006,

title = {Comparative genomics of stenotrophomonas maltophilia and stenotrophomonas rhizophila revealed characteristic features of both species},

author = { A. Piński and J. Żur and R. Hasterok and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087866006&doi=10.3390%2fijms21144922&partnerID=40&md5=d3558a7364b4d6e0f87930ba3345b45d},

doi = {10.3390/ijms21144922},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {14},

pages = {1-20},

publisher = {MDPI AG},

abstract = {Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g.; chitin-binding protein; mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g.; glucosylglycerol-phosphate synthase; cold shock protein with the DUF1294 domain; and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85079226601,

title = {A whole-cell immobilization system on bacterial cellulose for the paracetamol-degrading Pseudomonas moorei KB4 strain},

author = { J. Żur and A. Piński and J. Michalska and K.T. Hupert-Kocurek and A. Nowak and D. Wojcieszyńska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079226601&doi=10.1016%2fj.ibiod.2020.104919&partnerID=40&md5=83d05c44cb2a78963ef96e3d769f2088},

doi = {10.1016/j.ibiod.2020.104919},

issn = {09648305},

year  = {2020},

date = {2020-01-01},

journal = {International Biodeterioration and Biodegradation},

volume = {149},

publisher = {Elsevier Ltd},

abstract = {Microorganisms with a high natural ability to degrade xenobiotics, which are usually characterized by a diverse metabolism and unique features, can be used as natural biocatalysts in wastewater treatment or bioaugmentation processes. The immobilization of such strains greatly increases their stability and degradation properties. The most critical issues in designing whole-cell immobilization systems are selecting the suitable carrier and determining the bacterial features that will promote effective immobilization. In this study, we immobilized the paracetamol-degrading Pseudomonas moorei KB4 strain on the bacterial cellulose disks that were produced by Komagataeibacter xylinus E-89370. The KB4 strain immobilized on the cellulose degraded 150 mg L−1 of paracetamol in three series of 50 mg L−1 in each cycle. The average protein concentration and dehydrogenase activity increased after the degradation of each dose. The specific activity (U mg−1 of protein) of the main enzymes involved in the degradation pathway was 0.22 for deaminase, 5.1 for acylamidohydrolase and 3.49 for ring-cleavage hydroquinone 1,2-dioxygenase. The relative expression level of the genes encoding deaminases and acylamidohydrolases increased in the presence of paracetamol, though more prominently in the immobilized than in the free cells. © 2020 Elsevier Ltd},

note = {19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85063114635,

title = {A new pathway for naproxen utilisation by Bacillus thuringiensis B1(2015b) and its decomposition in the presence of organic and inorganic contaminants},

author = { D. Górny and U. Guzik and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063114635&doi=10.1016%2fj.jenvman.2019.03.034&partnerID=40&md5=74244b4c49f7546b44695325fb4d62f1},

doi = {10.1016/j.jenvman.2019.03.034},

issn = {03014797},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Environmental Management},

volume = {239},

pages = {1-7},

publisher = {Academic Press},

abstract = {Bacillus thuringiensis B1 (2015b) is a bacterial strain that is able to degrade naproxen. However, the potential effect of water co-contaminations on the degradation process and its pathway have not yet been evaluated. The results of our study show that in the presence of aromatic compounds, the B1 (2015b) strain utilised naproxen with an efficiency that was similar to what it was with no aromatic co-contaminations. In the presence of methanol, biodegradation of naproxen was inhibited, while the addition of ethanol increased the decomposition of naproxen. Among the metal ions that were tested, only cobalt (II) and cadmium (II) negatively affected the degradation of the drug. An analysis of the intermediates and enzymes that are engaged in degrading naproxen revealed that the key metabolites are O-desmethylnaproxen, which is the product of tetrahydrofolate-dependent O-demethylase activity, and salicylic acid. Salicylic acid can then be hydroxylated to catechol or gentisic acid or can be cleaved to 2-oxo-3,5-heptadienedioic acid. The high activity level of catechol 1,2-dioxygenase indicated that the main degradative pathway of naproxen in the B1 (2015b) strain is via catechol cleavage. © 2019 Elsevier Ltd},

note = {13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85065116283,

title = {Defining the genetic basis of plant–endophytic bacteria interactions},

author = { A. Piński and A. Betekhtin and K.T. Hupert-Kocurek and L.A.J. Mur and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85065116283&doi=10.3390%2fijms20081947&partnerID=40&md5=96b5990897aec8304bac8977b991dff7},

doi = {10.3390/ijms20081947},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {8},

publisher = {MDPI AG},

abstract = {Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {52},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85055336990,

title = {Naproxen ecotoxicity and biodegradation by Bacillus thuringiensis B1(2015b) strain},

author = { D. Górny and U. Guzik and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85055336990&doi=10.1016%2fj.ecoenv.2018.10.067&partnerID=40&md5=d2e8928875b3a10dfacc3bd31f5d8b0d},

doi = {10.1016/j.ecoenv.2018.10.067},

issn = {01476513},

year  = {2019},

date = {2019-01-01},

journal = {Ecotoxicology and Environmental Safety},

volume = {167},

pages = {505-512},

publisher = {Academic Press},

abstract = {High level of naproxen consumption leads to the appearance of this drug in the environment but its possible effects on non-target organisms together with its biodegradation are not well studied. The aim of this work was to evaluate naproxen ecotoxicity by using the Microbial Assay for Risk Assessment. Moreover, Bacillus thuringiensis B1(2015b) was tested for both ecotoxicity and the ability of this strain to degrade naproxen in cometabolic conditions. The results indicate that the mean value of microbial toxic concentration estimated by MARA test amounts to 1.66 g/L whereas EC50 of naproxen for B1(2015b) strain was 4.69 g/L. At toxic concentration, Bacillus thuringiensis B1(2015b) showed 16:0 iso 3OH fatty acid presence and an increase in the ratio of total saturated to unsaturated fatty acids. High resistance of the examined strain to naproxen correlated with its ability to degrade this drug in cometabolic conditions. The results of bacterial reverse mutation assay (Ames test) revealed that naproxen at concentrations above 1 g/L showed genotoxic effect but the response was not dose-dependent. Maximal specific naproxen removal rate was observed at pH 6.5 and 30 °C, and in the presence of 0.5 g/L glucose as a growth substrate. Kinetic analysis allowed estimation of the half saturation constant (Ks) and the maximum specific naproxen removal rate (qmax) as 6.86 mg/L and 1.26 mg/L day, respectively. These results indicate that Bacillus thuringiensis B1(2015b) has a high ability to degrade naproxen and is a potential tool for bioremediation. © 2018 Elsevier Inc.},

note = {33},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85048021599,

title = {Paracetamol – toxicity and microbial utilization. Pseudomonas moorei KB4 as a case study for exploring degradation pathway},

author = { J. Żur and D. Wojcieszyńska and K.T. Hupert-Kocurek and A. Marchlewicz and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048021599&doi=10.1016%2fj.chemosphere.2018.04.179&partnerID=40&md5=9941e36fe7554a810b10735fb721bbcc},

doi = {10.1016/j.chemosphere.2018.04.179},

issn = {00456535},

year  = {2018},

date = {2018-01-01},

journal = {Chemosphere},

volume = {206},

pages = {192-202},

publisher = {Elsevier Ltd},

abstract = {Paracetamol, a widely used analgesic and antipyretic drug, is currently one of the most emerging pollutants worldwide. Besides its wide prevalence in the literature only several bacterial strains able to degrade this compound have been described. In this study, we isolated six new bacterial strains able to remove paracetamol. The isolated strains were identified as the members of Pseudomonas, Bacillus, Acinetobacter and Sphingomonas genera and characterized phenotypically and biochemically using standard methods. From the isolated strains, Pseudomonas moorei KB4 was able to utilize 50 mg L−1 of paracetamol. As the main degradation products, p-aminophenol and hydroquinone were identified. Based on the measurements of specific activity of acyl amidohydrolase, deaminase and hydroquinone 1,2-dioxygenase and the results of liquid chromatography analyses, we proposed a mechanism of paracetamol degradation by KB4 strain under co-metabolic conditions with glucose. Additionally, toxicity bioassays and the influence of various environmental factors, including pH, temperature, heavy metals at no-observed-effective-concentrations, and the presence of aromatic compounds on the efficiency and mechanism of paracetamol degradation by KB4 strain were determined. This comprehensive study about paracetamol biodegradation will be helpful in designing a treatment systems of wastewaters contaminated with paracetamol. © 2018 Elsevier Ltd},

note = {63},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85048822480,

title = {Organic micropollutants paracetamol and ibuprofen—toxicity, biodegradation, and genetic background of their utilization by bacteria},

author = { J. Żur and A. Piński and A. Marchlewicz and K.T. Hupert-Kocurek and D. Wojcieszyńska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048822480&doi=10.1007%2fs11356-018-2517-x&partnerID=40&md5=bed6633cc8ff497e87e086da67cbead2},

doi = {10.1007/s11356-018-2517-x},

issn = {09441344},

year  = {2018},

date = {2018-01-01},

journal = {Environmental Science and Pollution Research},

volume = {25},

number = {22},

pages = {21498-21524},

publisher = {Springer Verlag},

abstract = {Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern. Moreover, to date, conventional wastewater treatment plants (WWTPs) are not fully adapted to remove that kind of micropollutants. Bioremediation processes, which utilize bacterial strains with increased degradation abilities, seem to be a promising alternative to the chemical methods used so far. Nevertheless, despite the wide prevalence of paracetamol and ibuprofen in the environment, toxicity and mechanism of their microbial degradation as well as genetic background of these processes remain not fully characterized. In this review, we described the current state of knowledge about toxicity and biodegradation mechanisms of paracetamol and ibuprofen and provided bioinformatics analysis concerning the genetic bases of these xenobiotics decomposition. © 2018, The Author(s).},

note = {90},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85048057032,

title = {Immobilization of Planococcus sp. S5 strain on the loofah sponge and its application in naproxen removal},

author = { A. Dzionek and D. Wojcieszyńska and K.T. Hupert-Kocurek and M. Adamczyk-Habrajska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048057032&doi=10.3390%2fcatal8050176&partnerID=40&md5=ae170a3a84ad2289b7ca0641afaad21c},

doi = {10.3390/catal8050176},

issn = {20734344},

year  = {2018},

date = {2018-01-01},

journal = {Catalysts},

volume = {8},

number = {5},

publisher = {MDPI},

abstract = {Planococcus sp. S5, a Gram-positive bacterium isolated from the activated sludge is known to degrade naproxen in the presence of an additional carbon source. Due to the possible toxicity of naproxen and intermediates of its degradation, the whole cells of S5 strain were immobilized onto loofah sponge. The immobilized cells degraded 6, 9, 12 or 15 mg/L of naproxen faster than the free cells. Planococcus sp. cells immobilized onto the loofah sponge were able to degrade naproxen efficiently for 55 days without significant damage and disintegration of the carrier. Analysis of the activity of enzymes involved in naproxen degradation showed that stabilization of S5 cells in exopolysaccharide (EPS) resulted in a significant increase of their activity. Changes in the structure of biofilm formed on the loofah sponge cubes during degradation of naproxen were observed. Developed biocatalyst system showed high resistance to naproxen and its intermediates and degraded higher concentrations of the drug in comparison to the free cells. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85010723117,

title = {Toxicity and biodegradation of ibuprofen by Bacillus thuringiensis B1(2015b)},

author = { A. Marchlewicz and U. Guzik and K.T. Hupert-Kocurek and A. Nowak and S. Wilczyńska and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010723117&doi=10.1007%2fs11356-017-8372-3&partnerID=40&md5=f8a6724832ad5bb834800f9207067ea7},

doi = {10.1007/s11356-017-8372-3},

issn = {09441344},

year  = {2017},

date = {2017-01-01},

journal = {Environmental Science and Pollution Research},

volume = {24},

number = {8},

pages = {7572-7584},

publisher = {Springer Verlag},

abstract = {In recent years, the increased intake of ibuprofen has resulted in the presence of the drug in the environment. This work presents results of a study on degradation of ibuprofen at 25 mg L−1 in the presence of glucose, as an additional carbon source by Bacillus thuringiensis B1(2015b). In the cometabolic system, the maximum specific growth rate of the bacterial strain was 0.07 ± 0.01 mg mL−1 h−1 and Ksμ 0.27 ± 0.15 mg L−1. The maximum specific ibuprofen removal rate and the value of the half-saturation constant were qmax = 0.24 ± 0.02 mg mL−1 h−1 and Ks = 2.12 ± 0.56 mg L−1, respectively. It has been suggested that monooxygenase and catechol 1,2-dioxygenase are involved in ibuprofen degradation by B. thuringiensis B1(2015b). Toxicity studies showed that B. thuringiensis B1(2015b) is more resistant to ibuprofen than other tested organisms. The EC50 of ibuprofen on the B1 strain is 809.3 mg L−1, and it is 1.5 times higher than the value of the microbial toxic concentration (MTCavg). The obtained results indicate that B. thuringiensis B1(2015b) could be a useful tool in biodegradation/bioremediation processes. © 2017, The Author(s).},

note = {37},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85021369406,

title = {Genomic analysis of plant-associated bacteria and their potential in enhancing phytoremediation efficiency},

author = { A. Piński and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021369406&doi=10.12911%2f22998993%2f74281&partnerID=40&md5=072bd8a796ca987e1fc16e2af5c5e52f},

doi = {10.12911/22998993/74281},

issn = {2081139X},

year  = {2017},

date = {2017-01-01},

journal = {Journal of Ecological Engineering},

volume = {18},

number = {4},

pages = {152-159},

publisher = {Polish Society of Ecological Engineering (PTIE)},

abstract = {Phytoremediation is an emerging technology that uses plants in order to cleanup pollutants including xenobiotics and heavy metals from soil, water and air. Inoculation of plants with plant growth promoting endophytic and rhizospheric bacteria can enhance efficiency of phytoremediation. Genomic analysis of four plant-associated strains belonging to the Stenotrophomonas maltophilia species revealed the presence of genes encoding proteins involved in plant growth promotion, biocontrol of phytopathogens, biodegradation of xenobiotics, heavy metals resistance and plant-bacteria-environment interaction. The results of this analysis suggest great potential of bacteria belonging to Stenotrophomonas maltophilia species in enhancing phytoremediation efficiency.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84964483982,

title = {Substitutions of conserved residues in the c-terminal region of DnaC cause thermolability in helicase loading},

author = { M.M. Felczak and J.M. Sage and K.T. Hupert-Kocurek and S. Aykul and J.M. Kaguni},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964483982&doi=10.1074%2fjbc.M115.708586&partnerID=40&md5=6d13be99774d88237272ccb5c1150eb7},

doi = {10.1074/jbc.M115.708586},

issn = {00219258},

year  = {2016},

date = {2016-01-01},

journal = {Journal of Biological Chemistry},

volume = {291},

number = {9},

pages = {4803-4812},

publisher = {American Society for Biochemistry and Molecular Biology Inc.},

abstract = {The DnaB-DnaC complex binds to the unwound DNA within the Escherichia coli replication origin in the helicase loading process, but the biochemical events that lead to its stable binding are uncertain. This study characterizes the function of specific C-terminal residues of DnaC. Genetic and biochemical characterization of proteins bearing F231S and W233L substitutions of DnaC reveals that their activity is thermolabile. Because the mutants remain able to form a complex with DnaB at 30 and 37 °C, their thermolability is not explained by an impaired interaction with DnaB. Photo-cross-linking experiments and biosensor analysis show an altered affinity of these mutants compared with wild type DnaC for single-stranded DNA, suggesting that the substitutions affect DNA binding. Despite this difference, their activity inDNAbinding is not thermolabile. The substitutions also drastically reduce the affinity of DnaC for ATP as measured by the binding of a fluorescent ATP analogue (MANT-ATP) and byUVcross-linking of radiolabeled ATP. Experiments show that an elevated temperature substantially inhibits both mutants in their ability to load the DnaBDnaCcomplex at aDnaAbox. Because a decreasedATPconcentration exacerbates their thermolabile behavior, we suggest that the F231S and W233L substitutions are thermolabile in ATP binding, which correlates with defective helicase loading at an elevated temperature. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85011672972,

title = {Genetic basis of endophytic bacteria-plant interactions [Genetyczne podłoze oddziałyawń bakterii endofitycznych z roslinami]},

author = { A. Piński and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85011672972&partnerID=40&md5=118d5da7c4e1d1f3c9c3477fb256b068},

issn = {00794252},

year  = {2016},

date = {2016-01-01},

journal = {Postepy Mikrobiologii},

volume = {55},

number = {4},

pages = {404-412},

publisher = {Polish Society of Microbiologists},

abstract = {Bacterial endophytes promote plant growth through colonization of the internal tissues of the plant without external signs of infection or negative effects on their host. Although endophytic bacteria enter the plant through the primary and lateral root hair cells, root cracks and wounds, they are found at many sites in the plants, such as stems, leaves, seeds, and xylem. The colonization of plant tissues comprises: host recognition, chemotactic migration of endophyte towards root exudates, adhesion to the surface of the root, penetration of the epidermidis and finally adaptation to a new environment. The distinctive features of endophytic bacteria are their flagellar motility, secretion of the cell-wall degrading enzymes (CWDEs) and biofilm-forming ability. It is postulated that endophytic bacteria capable of colonizing plants should contain at least a minimum set of genes responsible for their endophytic behavior. Among them, genes involved in chemotaxis and adhesion processes, secretion and translocation of effector proteins as well as genes which facilitate survival in reactiveoxygen rich environment can be distinguished. An important group of genes are the ones which encode regulatory proteins involved in the control of gene expression at the transcriptional level. However, in establishing an endophytic association with plants, species-specific gene-functions seem to be involved. Identification of genes responsible for endophytic behavior will increase our knowledge about the genetic aspects of plant-endophyte interactions and enable to fully exploit their potential.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84992727831,

title = {Toxicity of diclofenac and its biotransformation by Raoultella sp. DD4},

author = { D. Domaradzka and U. Guzik and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84992727831&doi=10.15244%2fpjoes%2f62681&partnerID=40&md5=28aa684d23e71c5a99cb3676c6892d13},

doi = {10.15244/pjoes/62681},

issn = {12301485},

year  = {2016},

date = {2016-01-01},

journal = {Polish Journal of Environmental Studies},

volume = {25},

number = {5},

pages = {2211-2216},

publisher = {HARD Publishing Company},

abstract = {In recent years the increased consumption of diclofenac, a biologically active compound that is toxic to organisms and persistent to biodegradation, has resulted in its presence in the environment. This is the first report on the biotransformation of diclofenac by a pure bacterial strain, Raoultella sp. DD4, which is able to transform 0.6 mg/L of diclofenac in 28 days. Additionally, strain DD4 is more resistant to diclofenac than other tested organisms. The estimated value for EC50 for this strain is 1.95 g/L. This is approximately five-fold higher than the value of microbial toxic concentration MTCavg (0.416 g/L). Moreover, genotoxicity studies have indicated that diclofenac is not a mutagenic compound. © 2016, HARD Publishing Company. All rights reserved.},

note = {15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84978405481,

title = {Enzymes involved in naproxen degradation by Planococcus sp. S5},

author = { D. Wojcieszyńska and D. Domaradzka and K.T. Hupert-Kocurek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84978405481&doi=10.5604%2f17331331.1204477&partnerID=40&md5=2691aff2112e1850d1b9042cb8b8f85f},

doi = {10.5604/17331331.1204477},

issn = {17331331},

year  = {2016},

date = {2016-01-01},

journal = {Polish Journal of Microbiology},

volume = {65},

number = {2},

pages = {177-182},

publisher = {Polish Society of Microbiologists},

abstract = {Naproxen is a one of the most popular non-steroidal anti-inflammatory drugs (NSAIDs) entering the environment as a result of high consumption. For this reason, there is an emerging need to recognize mechanisms of its degradation and enzymes engaged in this process. Planococcus sp. S5 is a gram positive strain able to degrade naproxen in monosubstrate culture (27%). However, naproxen is not a sufficient growth substrate for this strain. In the presence of benzoate, 4-hydroxybenzoic acid, 3,4-dihydroxybenzoic acid or vanillic acid as growth substrates, the degradation of 21.5%, 71.71%, 14.75% and 8.16% of naproxen was observed respectively. It was shown that the activity of monooxygenase, hydroxyquinol 1,2-dioxygenase, protocatechuate 3,4-dioxygenase and protocatechuate 4,5-dioxyegnase in strain S5 was induced after growth of the strain with naproxen and 4-hydroxybenzoate. Moreover, in the presence of naproxen activity of gentisate 1,2-dioxygenase, enzyme engaged in 4-hydroxybenzoate metabolism, was completely inhibited. The obtained results suggest that monooxygenase and hydroxyquinol 1,2-dioxygenase are the main enzymes in naproxen degradation by Planococcus sp. S5.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84940743637,

title = {A single amino acid substitution within catalytically non-active N-terminal domain of catechol 2,3-dioxygenase (C23O) increases enzyme activity towards 4-chlorocatechol},

author = { K.T. Hupert-Kocurek and D. Wojcieszyńska and U. Guzik and T. Borowski},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940743637&doi=10.1016%2fj.molcatb.2015.08.012&partnerID=40&md5=275aad1c1e7797a2d062496f181bdd67},

doi = {10.1016/j.molcatb.2015.08.012},

issn = {13811177},

year  = {2015},

date = {2015-01-01},

journal = {Journal of Molecular Catalysis B: Enzymatic},

volume = {122},

pages = {64-71},

publisher = {Elsevier},

abstract = {In this work we have shown for the first time the effect of Met65Thr substitution on the activity of catechol 2,3-dioxygenase (C23O) from Planococcus sp. strain S5. Even though the 3D model does not reveal the influence of an amino acid substitution on the enzyme active site structure, the Thr65 variant differed in lower pH optimum and lower Km from the wild type enzyme. Activity measurements with various catechols as the substrates showed almost 1.5-times higher activity of the mutant protein in comparison to the wild type enzyme against 4-methylcatechol and its remarkably high activity towards 4-chlorocatechol. From the computational studies it follows that the difference in activity of the wild type and mutant form of C23O towards 4-chlorocatechol is most likely linked to the shift of the pH optimum caused by the presence of the two additional H-bonds between Ser307 and Thr65 which anchor the C-terminal fragment of the protein. This work reveals the role of the N-terminal domain, which is considered to be catalytically inactive, in modulation of the C23O activity and the obtained results may facilitate the engineering of C23Os for bioremediation of environments contaminated with chloroaromatic compounds. © 2015 Elsevier B.V. All rights reserved.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84939420469,

title = {Cometabolic Degradation of Naproxen by Planococcus sp. Strain S5},

author = { D. Domaradzka and U. Guzik and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939420469&doi=10.1007%2fs11270-015-2564-6&partnerID=40&md5=c6345d970a9664b6683b8176b417f511},

doi = {10.1007/s11270-015-2564-6},

issn = {00496979},

year  = {2015},

date = {2015-01-01},

journal = {Water, Air, and Soil Pollution},

volume = {226},

number = {9},

publisher = {Kluwer Academic Publishers},

abstract = {Naproxen is a non-steroidal anti-inflammatory drug frequently detected in the influent and effluent of sewage treatment plants. The Gram-positive strain Planococcus sp. S5 was able to remove approximately 30 % of naproxen after 35 days of incubation in monosubstrate culture. Under cometabolic conditions, with glucose or phenol as a growth substrate, the degradation efficiency of S5 increased. During 35 days of incubation, 75.14∈±∈1.71 % and 86.27∈±∈2.09 % of naproxen was degraded in the presence of glucose and phenol, respectively. The highest rate of naproxen degradation observed in the presence of phenol may be connected with the fact that phenol is known to induce enzymes responsible for aromatic ring cleavage. The activity of phenol monooxygenase, naphthalene monooxygenase, and hydroxyquinol 1,2-dioxygenase was indicated in Planococcus sp. S5 culture with glucose or phenol as a growth substrate. It is suggested that these enzymes may be engaged in naproxen degradation. © 2015 The Author(s).},

note = {37},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84904109255,

title = {Bacterial degradation of naproxen - Undisclosed pollutant in the environment},

author = { D. Wojcieszyńska and D. Domaradzka and K.T. Hupert-Kocurek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904109255&doi=10.1016%2fj.jenvman.2014.06.023&partnerID=40&md5=8396bf85baa6f3cffdfdc91db000d0b7},

doi = {10.1016/j.jenvman.2014.06.023},

issn = {03014797},

year  = {2014},

date = {2014-01-01},

journal = {Journal of Environmental Management},

volume = {145},

pages = {157-161},

publisher = {Academic Press},

abstract = {The presence of non-steroidal anti-inflammatory drugs (NSAIDs) in the environment is an emerging problem due to their potential influence on human health and biocenosis. This is the first report on the biotransformation of naproxen, a polycyclic NSAID, by a bacterial strain. Stenotrophomonas maltophilia KB2 transformed naproxen within 35 days with about 28% degradation efficiency. Under cometabolic conditions with glucose or phenol as a carbon source degradation efficiency was 78% and 40%, respectively. Moreover, in the presence of naproxen phenol monooxygenase, naphthalene dioxygenase, hydroxyquinol 1,2-dioxygenase and gentisate 1,2-dioxygenase were induced. This suggests that degradation of naproxen occurs by its hydroxylation to 5,7,8-trihydroxynaproxen, an intermediate that can be cleaved by hydroxyquinol 1,2-dioxygenase. The cleavage product is probably further oxidatively cleaved by gentisate 1,2-dioxygenase. The obtained results provide the basis for the use of cometabolic systems in the bioremediation of polycyclic NSAID-contaminated environments. © 2014 Elsevier Ltd.},

note = {68},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84923059995,

title = {Altering substrate specificity of catechol 2,3-dioxygenase from Planococcus sp. strain S5 by random mutagenesis},

author = { K.T. Hupert-Kocurek and D. Wojcieszyńska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84923059995&partnerID=40&md5=583f83c3e86789051898035ee0a692d8},

issn = {0001527X},

year  = {2014},

date = {2014-01-01},

journal = {Acta Biochimica Polonica},

volume = {61},

number = {4},

pages = {705-710},

publisher = {Polskie Towarzystwo Biochemiczne},

abstract = {c23o gene, encoding catechol 2,3-dioxygenase from Planococcus sp. strain S5 was randomly mutagenized to generate variant forms of the enzyme with higher degradation activity. Additionally, the effect of introduced mutations on the enzyme structure was analyzed based on the putative 3D models the wild-type and mutant enzymes. C23OB58 and C23OB81 mutant proteins with amino acid substitutions in close proximity to the enzyme surface or at the interface and in the vicinity of the enzyme active site respectively showed the lowest activity towards all catecholic substrates. The relative activity of C23OC61 mutant towards para-substituted catechols was 20-30% lower of the wild-type enzyme. In this mutant all changes: F191I, C268R, Y272H, V280A and Y293D were located within the conserved regions of C-terminal domain. From these F191I seems to have significant implications for enzyme activity. The highest activity towards different catechols was found for mutant C23OB65. R296Q mutation improved the activity of C23O especially against 4-chlorocatechol. The relative activity of above-mentioned mutant detected against this substrate was almost 6-fold higher than the wild-type enzyme. These results should facilitate future engineering of the enzyme for bioremediation.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84904793107,

title = {Immobilization as a strategy for improving enzyme properties- Application to oxidoreductases},

author = { U. Guzik and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904793107&doi=10.3390%2fmolecules19078995&partnerID=40&md5=5182d5114ec3a4f8a2b47ed06ec70d6a},

doi = {10.3390/molecules19078995},

issn = {14203049},

year  = {2014},

date = {2014-01-01},

journal = {Molecules},

volume = {19},

number = {7},

pages = {8995-9018},

publisher = {MDPI AG},

abstract = {The main objective of the immobilization of enzymes is to enhance the economics of biocatalytic processes. Immobilization allows one to re-use the enzyme for an extended period of time and enables easier separation of the catalyst from the product. Additionally, immobilization improves many properties of enzymes such as performance in organic solvents, pH tolerance, heat stability or the functional stability. Increasing the structural rigidity of the protein and stabilization of multimeric enzymes which prevents dissociation-related inactivation. In the last decade, several papers about immobilization methods have been published. In our work, we present a relation between the influence of immobilization on the improvement of the properties of selected oxidoreductases and their commercial value. We also present our view on the role that different immobilization methods play in the reduction of enzyme inhibition during biotechnological processes.},

note = {352},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84902906788,

title = {Protocatechuate 3,4-dioxygenase: A wide substrate specificity enzyme isolated from stenotrophomonas maltophilia kb2 as a useful tool in aromatic acid biodegradation},

author = { U. Guzik and K.T. Hupert-Kocurek and M. Sitnik and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84902906788&doi=10.1159%2f000362791&partnerID=40&md5=5f82d3db26962e7883a672ef42262ad1},

doi = {10.1159/000362791},

issn = {14641801},

year  = {2014},

date = {2014-01-01},

journal = {Journal of Molecular Microbiology and Biotechnology},

volume = {24},

number = {3},

pages = {150-160},

publisher = {S. Karger AG},

abstract = {Protocatechuate 3,4-dioxygenases (P34Os) catalyze the reaction of the ring cleavage of aromatic acid derivatives. It is a key reaction in many xenobiotic metabolic pathways. P34Os characterize narrow substrate specificity. This property is an unfavorable feature in the biodegradation process because one type of pollution is rarely present in the environment. Thus, the following study aimed at the characterization of a P34O from Stenotrophomonas maltophilia KB2, being able to utilize a wide spectrum of aromatic carboxylic acids. A total of 3 mM vanillic acid and 4-hydroxybenzoate were completely degraded during 8 and 4.5 h, respectively. When cells of strain KB2 were grown on 9 mM 4-hydroxybenzoate, P34O was induced. Biochemical analysis revealed that the examined enzyme was similar to other known P34Os, but showed untypical wide substrate specificity. A high activity of P34O against 2,4-and 3,5-dihydroxybenzoate was observed. As these substrates do not possess ortho configuration hydroxyl groups, it is postulated that their cleavage could be connected with their monodentate binding of substrate to the active site. Since this enzyme characterizes untypical wide substrate specificity it makes it a useful tool in applications for environmental clean-up purposes. © 2014 S. Karger AG, Basel.},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84900542945,

title = {Microbial degradation non-steroidal anti-inflammatory drugs [Mikrobiologiczna degradacja niesteroidowych leków przeciwzapalnych]},

author = { U. Guzik and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84900542945&partnerID=40&md5=5f88d768025e13d5c3de1fb8fb1e8b59},

issn = {00794252},

year  = {2014},

date = {2014-01-01},

journal = {Postepy Mikrobiologii},

volume = {53},

number = {1},

pages = {61-69},

publisher = {Polish Society of Microbiologists},

abstract = {In the recent years, commonly used non-steroidal anti-inflammatory drugs (NSAIDs) are widely detected in the environment. These biologically active substances and their continuous inflow into the environment may lead to their accumulation in the environment and chronic exposure of organisms. This in turn may cause the potential negative effects on living organisms. While the transformation mechanisms of non-steroidal anti-inflammatory drugs in the human body and in other animals have been extensively studied, degradation of these drugs by bacteria (including their degradation pathways and degradation products) has seldom been investigated and are largely unknown. Therefore, the objective of this paper is presentation actual stage of knowledge about microbiological degradation pathways of NSAIDs such as naproxen, ibuprofen, diclofenac, paracetamol.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84900540401,

title = {Directed evolution of microbial enzymes [Ukierunkowana ewolucja enzymów pochodzenia mikrobiologicznego]},

author = { K.T. Hupert-Kocurek and A. Banaś and D. Wojcieszyńska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84900540401&partnerID=40&md5=5c7b16858f67f10bb0d6751ffd78290b},

issn = {00794252},

year  = {2014},

date = {2014-01-01},

journal = {Postepy Mikrobiologii},

volume = {53},

number = {1},

pages = {43-48},

publisher = {Polish Society of Microbiologists},

abstract = {Enzymes of microbial origin are extensively used in different industrial processes. However, very often these biocatalysts do not meet the requirements for a large-scale application and its properties have to be optimized. This includes not only the chemoselectivity, regioselectivity and stereoselectivity, but also long-term stability of the biocatalyst at certain temperatures or pH-values and activity in the presence of high substrate concentrations. Protein engineering has emerged as an important tool to overcome the limitations of natural enzymes as biocatalysts. There are two general strategies for protein engineering, rational design and directed evolution. In rational design detailed knowledge of the structure and function of the protein is used to make desired changes. Directed evolution involves either a random mutagenesis of the gene encoding the enzyme (e.g. by error-prone PCR) or recombination of gene fragments derived from DNase degradation, random priming recombination, random chimeragenesis on transient templates or recombined extension on truncated templates. In this review the essential methods for directed evolution of enzymes are described and various examples for the application of these protein engineering tools are provided.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84896333493,

title = {Activity of a carboxyl-terminal truncated form of catechol 2,3-dioxygenase from Planococcus sp. S5},

author = { K.T. Hupert-Kocurek and D. Wojcieszyńska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896333493&doi=10.1155%2f2014%2f598518&partnerID=40&md5=0cf405fd62db07759b5d5d007c553600},

doi = {10.1155/2014/598518},

issn = {1537744X},

year  = {2014},

date = {2014-01-01},

journal = {The Scientific World Journal},

volume = {2014},

publisher = {ScientificWorld Ltd.},

abstract = {Catechol 2,3-dioxygenases (C23Os; E.C.1.13.12.2) are two domain enzymes that catalyze degradation of monoaromatic hydrocarbons. The catalytically active C-domain of all known C23Os comprises ferrous ion ligands as well as residues forming active site pocket. The aim of this work was to examine and discuss the effect of nonsense mutation at position 289 on the activity of catechol 2,3-dioxygenase from Planococcus strain. Although the mutant C23O showed the same optimal temperature for activity as the wild-type protein (35°C), it exhibited activity slightly more tolerant to alkaline pH. Mutant enzyme exhibited also higher affinity to catechol as a substrate. Its K m (66.17 μM) was approximately 30% lower than that of wild-type enzyme. Interestingly, removal of the C-terminal residues resulted in 1.5- to 1.8-fold (P < 0.05) increase in the activity of C23OB61 against 4-methylcatechol and 4-chlorocatechol, respectively, while towards catechol the activity of the protein dropped to about 80% of that of the wild-type enzyme. The results obtained may facilitate the engineering of the C23O for application in the bioremediation of polluted areas. © 2014 Katarzyna Hupert-Kocurek et al.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84896328434,

title = {Enhancement of biodegradation potential of catechol 1,2-dioxygenase through its immobilization in calcium alginate gel},

author = { U. Guzik and K.T. Hupert-Kocurek and A. Marchlewicz and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896328434&doi=10.1016%2fj.ejbt.2014.02.001&partnerID=40&md5=bc1dbc1301015a0aa17997acb14c24e0},

doi = {10.1016/j.ejbt.2014.02.001},

issn = {07173458},

year  = {2014},

date = {2014-01-01},

journal = {Electronic Journal of Biotechnology},

volume = {17},

number = {2},

pages = {83-88},

publisher = {Electronic Journal of Biotechnology},

abstract = {Background:In biodegradation processes free enzymes often undergo deactivation. Thus, it is very important to obtain highly stable enzymes by different methods. Immobilization allows for successful stabilization of many multimeric enzymes by increasing the rigidity of the enzyme structure. This study aimed to evaluate some environmental factors that affect catechol 1,2-dioxygenase from Stenotrophomonas maltophilia KB2 immobilized in alginate hydrogel. The goal of the present work was to improve the functional stability of the enzyme by increas-ing its structural rigidity.Results:Immobilization yield and expressed activity were 100% and 56%, respectively. Under the same storage conditions, the activity of the immobilized enzyme was still observed on the 28th day of incubation at 4 °C, whereas the free enzyme lost its activity after 14 days. The immobilized enzyme required approximately 10 °C lower temperature for its optimal activity than the free enzyme. Immobilization shifted the optimal pH from 8 for the soluble enzyme to 7 for the immobilized enzyme. The immobilized catechol 1,2-dioxygenase showed ac-tivity against 3-methylcatechol, 4-methylcatechol, 3-chlorocatechol, 4-chlorocatechol, and 3,5-dichlorocatechol. The immobilization of the enzyme promoted its stabilization against any distorting agents:aliphatic alcohols, phenols, and chelators.Conclusions:The entrapment of the catechol 1,2-dioxygenase from S. maltophilia KB2 has been shown to be an effective method for improving the functional properties of the enzyme. Increased resistance to inactivation by higher substrate concentration and other factors affecting enzyme activity as well as broadened substrate spec-ificity compared to the soluble enzyme. makes the immobilized catechol 1,2-dioxygenase suitable for the biore-mediation and detoxification of xenobiotic-contaminated environments. © 2014 Pontificia Universidad Católica de Valparaiso. Production and hosting by Elsevier B.V.All rights reserved.},

note = {38},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84896106164,

title = {Degradation potential of protocatechuate 3,4-dioxygenase from crude extract of Stenotrophomonas maltophilia strain KB2 immobilized in calcium alginate hydrogels and on glyoxyl agarose},

author = { U. Guzik and K.T. Hupert-Kocurek and M. Krysiak and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896106164&doi=10.1155%2f2014%2f138768&partnerID=40&md5=a294b2c485472dba4d58232c4766944d},

doi = {10.1155/2014/138768},

issn = {23146133},

year  = {2014},

date = {2014-01-01},

journal = {BioMed Research International},

volume = {2014},

publisher = {Hindawi Publishing Corporation},

abstract = {Microbial intradiol dioxygenases have been shown to have a great potential for bioremediation; however, their structure is sensitive to various environmental and chemical agents. Immobilization techniques allow for the improvement of enzyme properties. This is the first report on use of glyoxyl agarose and calcium alginate as matrixes for the immobilization of protocatechuate 3,4-dioxygenase. Multipoint attachment of the enzyme to the carrier caused maintenance of its initial activity during the 21 days. Immobilization of dioxygenase in calcium alginate or on glyoxyl agarose resulted in decrease in the optimum temperature by 5°C and 10°C, respectively. Entrapment of the enzyme in alginate gel shifted its optimum pH towards high-alkaline pH while immobilization of the enzyme on glyoxyl agarose did not influence pH profile of the enzyme. Protocatechuate 3,4-dioygenase immobilized in calcium alginate showed increased activity towards 2,5-dihydroxybenzoate, caffeic acid, 2,3-dihydroxybenzoate, and 3,5-dihydroxybenzoate. Slightly lower activity of the enzyme was observed after its immobilization on glyoxyl agarose. Entrapment of the enzyme in alginate gel protected it against chelators and aliphatic alcohols while its immobilization on glyoxyl agarose enhanced enzyme resistance to inactivation by metal ions. © 2014 Urszula Guzik et al.},

note = {29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84886592804,

title = {Cadmium increases catechol 2,3-dioxygenase activity in Variovorax sp. 12S, a metal-tolerant and phenol-degrading strain},

author = { K.T. Hupert-Kocurek and A. Saczyńska and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84886592804&doi=10.1007%2fs10482-013-9997-y&partnerID=40&md5=ba31ec309fe2261131dc2c0cd59e1f3f},

doi = {10.1007/s10482-013-9997-y},

issn = {00036072},

year  = {2013},

date = {2013-01-01},

journal = {Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology},

volume = {104},

number = {5},

pages = {845-853},

abstract = {A Gram-negative bacterium, designated as strain 12S, was isolated from a heavy metal-polluted soil. According to the biochemical characteristics, FAME analysis, and 16S rRNA gene sequence analysis, the isolated strain was identified as Variovorax sp. 12S. In the presence of 0.1 mM cadmium, 12S was able to completely utilize up to 1.5 mM of phenol as the sole carbon and energy source in an MSM-TRIS medium. Degradation of phenol was accompanied by a slow bacterial growth rate and an extension of the lag phase. The cells grown on phenol showed catechol 2,3-dioxygenase (C23O) activity. The activity of C23O from 12S cultivated in medium with Cd2+ was almost 20 % higher than in the control. Since environmental contamination with aromatic compounds is often accompanied by the presence of heavy metals, Variovorax sp. 12S and its C23O appear to be very powerful and useful tools in the biotreatment of wastewaters and soil decontamination. © 2013 Springer Science+Business Media Dordrecht.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84886902253,

title = {Original research influence of the entrapment of catechol 2, 3-dioxygenase in K-carrageenan on its properties},

author = { D. Wojcieszyńska and K.T. Hupert-Kocurek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84886902253&partnerID=40&md5=cda5edce73b129f04c79b1e44f10af3d},

issn = {12301485},

year  = {2013},

date = {2013-01-01},

journal = {Polish Journal of Environmental Studies},

volume = {22},

number = {4},

pages = {1219-1225},

abstract = {Microbial extradiol dioxygenases have a great potential in bioremediation, but their structure is very sensitive to various environmental and chemical agents. Immobilization techniques make the enzyme properties' improvement possible. This is the first report of the usage of κ-carrageenan as a matrix for the immobilization of catechol 2, 3-dioxygenase. The storage stability of entrapped catechol 2, 3-dioxygenase from Stenotrophomonas maltophilia KB2 in K-carrageenan hydrogel at 4°C was found up to 14 days, while the free enzyme lost its activity within 24 hours. The immobilization of dioxygenase decreased the optimum temperature by 10°C, while both soluble and immobilized enzyme showed similar pH properties. The Km, V max' and Hill constant values for the immobilized enzyme were 0.17 μM, 106.68 mU, and 1.00, respectively. The immobilized catechol 2, 3-dioxygenase showed higher activity against 3-methylcatechol, hydroquinone, and tetrachlorohydroquinone than the soluble enzyme. Immobilization of catechol 2, 3-dioxygenase protected the enzyme from inhibition and enhanced its resistance to inactivation during catalysis.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84880999628,

title = {Cloning and Mutagenesis of Catechol 2,3-Dioxygenase Gene from the Gram-Positive Planococcus sp. Strain S5},

author = { K.T. Hupert-Kocurek and A. Stawicka and D. Wojcieszyska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880999628&doi=10.1159%2f000351511&partnerID=40&md5=91b92f4bbbc7a36ad0c92750f0550129},

doi = {10.1159/000351511},

issn = {14641801},

year  = {2013},

date = {2013-01-01},

journal = {Journal of Molecular Microbiology and Biotechnology},

volume = {23},

number = {6},

pages = {381-390},

abstract = {In this study, the catechol 2,3-dioxygenase gene that encodes a 307-amino-acid protein was cloned from Planococcus sp. S5. The protein was identified to be a member of the superfamily I, subfamily 2A of extradiol dioxygenases. In order to study residues and regions affecting the enzyme's catalytic parameters, the c23o gene was randomly mutated by error-prone PCR. The wild-type enzyme and mutants containing substitutions within either the C-terminal or both domains were functionally produced in Escherichia coli and their activity towards catechol was characterized. The C23OB65 mutant with R296Q substitution showed significant tolerance to acidic pH with an optimum at pH 5.0. In addition, it showed activity more than 1.5 as high as that of the wild type enzyme and its K m was 2.5 times lower. It also showed altered sensitivity to substrate inhibition. The results indicate that residue at position 296 plays a role in determining pH dependence of the enzyme and its activity. Lower activity toward catechol was shown for mutants C23OB58 and C23OB81. Despite lower activity, these mutants showed higher affinity to catechol and were more sensitive to substrate concentration than nonmutated enzyme. Copyright © 2013 S. Karger AG, Basel.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84880412155,

title = {Microbiological degradation of cinnamic acid and its hydroxyl-derivatives [Mikrobiologiczny rozkład kwasu cynamonowego i jego hydroksypochodnych]},

author = { D. Wojcieszyńska and K.T. Hupert-Kocurek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880412155&partnerID=40&md5=263b0c3101f164e4545c723d556bd0bb},

issn = {00794252},

year  = {2013},

date = {2013-01-01},

journal = {Postepy Mikrobiologii},

volume = {52},

number = {2},

pages = {135-141},

abstract = {Microbiological degradation of cinnamic acid and its hydroxyl-derivatives occurs via aerobic or anaerobic pathway. The first step in the biodegradation of these compounds, both aerobic and anaerobic, is β-oxidation. The key intermediate in this process is benzoyl-CoA. In anaerobic environment this intermediate can be transformed to acetyl-CoA, incorporated into the central metabolism. Under aerobic condition benzoyl-CoA is transformed to protocatechuate acid, gentisic acid or catechol, compounds which are cleaved by a specific dioxygenase. Many microorganisms can transform phenolic acid to an amino acid or other compounds such as which 4-hydroxybenzoic acid, amide, acetophenone, which can be used in industry.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84878773526,

title = {Factors affecting activity of catechol 2,3-dioxygenase from 2-chlorophenol-degrading Stenotrophomonas maltophilia strain KB2},

author = { D. Wojcieszyńska and K.T. Hupert-Kocurek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84878773526&doi=10.3109%2f10242422.2013.796456&partnerID=40&md5=10f2c988ff519061818471fe0cee20d2},

doi = {10.3109/10242422.2013.796456},

issn = {10242422},

year  = {2013},

date = {2013-01-01},

journal = {Biocatalysis and Biotransformation},

volume = {31},

number = {3},

pages = {141-147},

abstract = {The effect of phenol on 2-chloro-and 2,4-dichlorophenol degradation by Stenotrophomonas maltophilia KB2 has been studied. During this study, we observed induction of catechol 2,3-dioxygenase (C23O). Since, in the environment, compounds which inhibit C23O activity are frequently present together with the main dioxygenase substrates, the main aim of this work was to determine the influence of various inhibitors and activators on the enzyme activity. Hydrogen peroxide of 60 μM concentration caused total inhibition of the enzyme. Addition of ascorbic acid suppressed the inhibitory effect of hydrogen peroxide. In its presence, 60 μM hydrogen peroxide caused only 40% inhibition of C23O activity. A positive effect in preventing C23O activity was observed also in the presence of chelators (8-hydroxyquinoline; EDTA; and phenanthroline). Most metal ions and aliphatic and aromatic hydroxylated derivatives caused a 20-40% decrease in enzyme activity. The results obtained indicate that C23O from Stenotrophomonas maltophilia strain KB2 holds great potential for bioremediation. © 2013 Informa UK, Ltd.},

note = {19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84878300907,

title = {High activity catechol 1,2-dioxygenase from Stenotrophomonas maltophilia strain KB2 as a useful tool in cis,cis-muconic acid production},

author = { U. Guzik and K.T. Hupert-Kocurek and M. Sitnik and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84878300907&doi=10.1007%2fs10482-013-9910-8&partnerID=40&md5=7ce52572f3232df5ba623a1babae57c1},

doi = {10.1007/s10482-013-9910-8},

issn = {00036072},

year  = {2013},

date = {2013-01-01},

journal = {Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology},

volume = {103},

number = {6},

pages = {1297-1307},

abstract = {This is the first report of a catechol 1,2-dioxygenase from Stenotrophomonas maltophilia strain KB2 with high activity against catechol and its methyl derivatives. This enzyme was maximally active at pH 8.0 and 40 C and the half-life of the enzyme at this temperature was 3 h. Kinetic studies showed that the value of K m and V max was 12.8 μM and 1,218.8 U/mg of protein, respectively. During our studies on kinetic properties of the catechol 1,2-dioxygenase we observed substrate inhibition at >80 μM. The nucleotide sequence of the gene encoding the S. maltophilia strain KB2 catechol 1,2-dioxygenase has high identity with other catA genes from members of the genus Pseudomonas. The deduced 314-residue sequence of the enzyme corresponds to a protein of molecular mass 34.5 kDa. This enzyme was inhibited by competitive inhibitors (phenol derivatives) only by ca. 30 %. High tolerance against condition changes is desirable in industrial processes. Our data suggest that this enzyme could be of use as a tool in production of cis,cis-muconic acid and its derivatives. © 2013 The Author(s).},

note = {43},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84877246424,

title = {Cinnamic acid and its hydroxy derivatives. Synthesis and application [Kwas cynamonowy i jego hydroksypochodne. Synteza i praktyczne zastosowania]},

author = { U. Guzik and K.T. Hupert-Kocurek and P. Siupka and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84877246424&partnerID=40&md5=0b74e0b28297a7e939a1f5cef04d4779},

issn = {00332496},

year  = {2013},

date = {2013-01-01},

journal = {Przemysl Chemiczny},

volume = {92},

number = {4},

pages = {458-462},

abstract = {A review, with 39 refs., of methods for chem. and biochem. synthesis of cinnamic, p-cumaric and 2,3-dihydroxycinnamic acids as well as their further enzymatic conversion to the org. intermediates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84874217080,

title = {Influence of metal ions on bioremediation activity of protocatechuate 3,4-dioxygenase from Stenotrophomonas maltophilia KB2},

author = { U. Guzik and K.T. Hupert-Kocurek and K. Sałek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84874217080&doi=10.1007%2fs11274-012-1178-z&partnerID=40&md5=86f3dd431848ce37007a515dd5292ff3},

doi = {10.1007/s11274-012-1178-z},

issn = {09593993},

year  = {2013},

date = {2013-01-01},

journal = {World Journal of Microbiology and Biotechnology},

volume = {29},

number = {2},

pages = {267-273},

publisher = {Kluwer Academic Publishers},

abstract = {The aim of this paper was to describe the effect of various metal ions on the activity of protocatechuate 3,4-dioxygenase from Stenotrophomonas maltophilia KB2. We also compared activity of different dioxygenases isolated from this strain, in the presence of metal ions, after induction by various aromatic compounds. S. maltophilia KB2 degraded 13 mM 3,4-dihydroxybenzoate, 10 mM benzoic acid and 12 mM phenol within 24 h of incubation. In the presence of dihydroxybenzoate and benzoate, the activity of protocatechuate 3,4-dioxygenase and catechol 1,2-dioxygenase was observed. Although Fe3+, Cu2+, Zn2+, Co2+, Al3+, Cd2+, Ni2+ and Mn2+ ions caused 20-80 % inhibition of protocatechuate 3,4-dioxygenase activity, the above-mentioned metal ions (with the exception of Ni2+) inhibited catechol 1,2-dioxygenase to a lesser extent or even activate the enzyme. Retaining activity of at least one of three dioxygenases from strain KB2 in the presence of metal ions makes it an ideal bacterium for bioremediation of contaminated areas. © 2012 The Author(s).},

note = {18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84873602961,

title = {Modern research methods for determining structures of intradiol dioxygenases},

author = { D. Wojcieszyńska and K.T. Hupert-Kocurek and M. Sitnik and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873602961&partnerID=40&md5=6b3050b542ed55718620248ffa34b80c},

issn = {00092886},

year  = {2012},

date = {2012-01-01},

journal = {Chemik},

volume = {66},

number = {12},

pages = {1346-1351},

abstract = {[No abstract available]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84860695543,

title = {Properties of catechol 2,3-dioxygenase from crude extract of Stenotrophomonas maltophilia strain KB2 immobilized in calcium alginate hydrogels},

author = { D. Wojcieszyńska and K.T. Hupert-Kocurek and A. Jankowska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84860695543&doi=10.1016%2fj.bej.2012.04.008&partnerID=40&md5=14ce296ada4edc670232a088b10ab730},

doi = {10.1016/j.bej.2012.04.008},

issn = {1369703X},

year  = {2012},

date = {2012-01-01},

journal = {Biochemical Engineering Journal},

volume = {66},

pages = {1-7},

abstract = {In this paper we report the immobilization of catechol 2,3-dioxygenase from Stenotrophomonas maltophilia KB2 in alginate hydrogel with the aim of improving its functional stability by increasing structural rigidity of the enzyme. Immobilization yield and expressed activity were 49.4% and 49.4%, respectively. The storage stability of entrapped catechol 2,3-dioxygenase at 4°C was found up to 35 days (266.3mU/mg protein), while at 4°C the free enzyme lost its activity within 24h. Immobilization of dioxygenase increased the optimum temperature for activity by 10°C, while both soluble and immobilized enzyme showed maximum activity at the same pH. The K m, V max, and Hill constant values for immobilized enzyme were 0.2μM, 604.6mU/mg protein, and 1.00, respectively, whereas those for the free enzyme were 46.3μM, 1602.0mU/mg protein, and 4.1, respectively.The immobilized catechol 2,3-dioxygenase from KB2 strain showed relatively higher activity against 3-methylcatechol, 4-methylcatechol, 4,5-dichlorocatechol, 3,5-dichlorocatechol, hydroquinone and tetrachlorohydroquinone than soluble enzyme. Immobilization of catechol 2,3-dioxygenase from KB2 strain protected the enzyme from the inhibition and enhanced its resistance to inactivation during catalysis. That makes the enzyme suitable for the bioremediation and detoxification of xenobiotic-contaminated environments. © 2012 Elsevier B.V.},

note = {47},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84873735799,

title = {Characterization of catechol 2,3-dioxygenase from Planococcus sp. Strain S5 induced by high phenol concentration},

author = { K.T. Hupert-Kocurek and U. Guzik and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873735799&doi=10.18388%2fabp.2012_2119&partnerID=40&md5=3f041e2a5c776d1ff6b9128cb2de66d0},

doi = {10.18388/abp.2012_2119},

issn = {0001527X},

year  = {2012},

date = {2012-01-01},

journal = {Acta Biochimica Polonica},

volume = {59},

number = {3},

pages = {345-351},

publisher = {Acta Biochimica Polonica},

abstract = {This study aimed at characterization of a new catechol 2,3-dioxygenase isolated from a Gram-positive bacterium able to utilize phenol as the sole carbon and energy source. Planococcus sp. strain S5 grown on 1 or 2 mM phenol showed activity of both a catechol 1,2- and catechol 2,3-dioxygenase while at a higher concentrations of phenol only catechol 2,3-dioxygenase activity was observed. The enzyme was optimally active at 60oC and pH 8.0. Kinetic studies showed that the Km and Vmax of the enzyme were 42.70 μM and 329.96 mU, respectively. The catechol 2,3-dioxygenase showed the following relative meta-cleavage activities for various catechols tested: catechol (100%), 3-methylcatechol (13.67%), 4-methylcatechol (106.33%) and 4-chlorocatechol (203.80%). The high reactivity of this enzyme towards 4-chlorocatechol is different from that observed for other catechol 2,3-dioxygenases. Nucleotide sequencing and homology search revealed that the gene encoding the S5 catechol 2,3-dioxygenase shared the greatest homology with the known genes encoding isoenzymes from Gram-negative Pseudomonas strains.},

note = {49},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84871698384,

title = {Flavin-dependent enzymes in cancer prevention},

author = { D. Wojcieszyńska and K.T. Hupert-Kocurek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84871698384&doi=10.3390%2fijms131216751&partnerID=40&md5=b25adf177d623e0f4756ba5f2245acb6},

doi = {10.3390/ijms131216751},

issn = {16616596},

year  = {2012},

date = {2012-01-01},

journal = {International Journal of Molecular Sciences},

volume = {13},

number = {12},

pages = {16751-16768},

publisher = {MDPI AG},

abstract = {Statistical studies have demonstrated that various agents may reduce the risk of cancer's development. One of them is activity of flavin-dependent enzymes such as flavin-containing monooxygenase (FMO)GS-OX1, FAD-dependent 5,10-methylenetetrahydrofolate reductase and flavin-dependent monoamine oxidase. In the last decade, many papers concerning their structure, reaction mechanism and role in the cancer prevention were published. In our work, we provide a more in-depth analysis of flavin-dependent enzymes and their contribution to the cancer prevention. We present the actual knowledge about the glucosinolate synthesized by flavin-containing monooxygenase (FMO)GS-OX1 and its role in cancer prevention, discuss the influence of mutations in FAD-dependent 5,10-methylenetetrahydrofolate reductase on the cancer risk, and describe FAD as an important cofactor for the demethylation of histons. We also present our views on the role of riboflavin supplements in the prevention against cancer. © 2012 by the authors; licensee MDPI, Basel, Switzerland.},

note = {14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-80052438366,

title = {Microbial degradation of chlorophenols, hazardous wastes of chemical industry [Mikrobiologiczny rozkład chlorofenoli, uciaz•liwych odpadów przemyłu chemicznege]},

author = { D. Wojcieszyńska and U. Guzik and K.T. Hupert-Kocurek and P. Siupka},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80052438366&partnerID=40&md5=cbe5c3b9fad5e79642baf6df3e961fb0},

issn = {00332496},

year  = {2011},

date = {2011-01-01},

journal = {Przemysl Chemiczny},

volume = {90},

number = {8},

pages = {1515-1519},

abstract = {A review, with 56 refs., of metabolic path ways for biochem. degrdn. of persistant Cl-contg. phenols, esp. via resp. chlorocatechols.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-79961208826,

title = {High activity catechol 2,3-dioxygenase from the cresols - Degrading Stenotrophomonas maltophilia strain KB2},

author = { D. Wojcieszyńska and K.T. Hupert-Kocurek and I. Greń and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79961208826&doi=10.1016%2fj.ibiod.2011.06.006&partnerID=40&md5=d6ef4d868b72531ce18499c1a567eb7c},

doi = {10.1016/j.ibiod.2011.06.006},

issn = {09648305},

year  = {2011},

date = {2011-01-01},

journal = {International Biodeterioration and Biodegradation},

volume = {65},

number = {6},

pages = {853-858},

abstract = {This study aimed at characterization of catechol 2,3-dioxygenase from Stenotrophomonas maltophilia KB2, being able to utilize a wide spectrum of aromatic substrates as a sole carbon and energy source. 2-methylphenol, 3-methylphenol, and 4-methylphenol was completely degraded during 24 h in concentration 6 mM, 7 mM, and 5 mM, respectively. When cells of strain KB2 were growing on methylphenols, catechol 2,3-dioxygenase was induced. Biochemical analysis revealed that the examined enzyme was similar to another catechol 2,3-dioxygenases, but showed extremely high activity. The enzyme was optimally active at 30 °C and pH 7.6. Kinetic studies showed that the value of Km, Vmax and Hill constant was 85.11 μM, 3.08 μM min-1 and 4.09 respectively. Comparative structural and phylogenetic analysis of catechol 2,3-dioxygenase from S. maltophilia KB2 had placed the protein with the single-ring substrate subfamily of the extradiol dioxygenase. We observed the presence of externally located α-helices and internally located β-sheets. We also suggest that the Fe2+ ion binding is facilitated via four ligands: two histidine residues, one glutamate residue and one molecule of water. © 2011 Elsevier Ltd.},

note = {31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-79953107665,

title = {Catechol 1,2-dioxygenase from the new aromatic compounds - Degrading Pseudomonas putida strain N6},

author = { U. Guzik and I. Greń and K.T. Hupert-Kocurek and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953107665&doi=10.1016%2fj.ibiod.2011.02.001&partnerID=40&md5=7fa3eb471f0eb2071b4a850b40265e4b},

doi = {10.1016/j.ibiod.2011.02.001},

issn = {09648305},

year  = {2011},

date = {2011-01-01},

journal = {International Biodeterioration and Biodegradation},

volume = {65},

number = {3},

pages = {504-512},

abstract = {This study aimed to characterization of catechol 1,2-dioxygenase from a Gram-negative bacterium, being able to utilize a wide spectrum of aromatic substrates as a sole carbon and energy source. Strain designated as N6, was isolated from the activated sludge samples of a sewage treatment plant at Bentwood Furniture Factory Jasienica, Poland. Morphology, physio-biochemical characteristics and phylogenetic analysis based on 16S rDNA sequence indicate that strain belongs to Pseudomonas putida. When cells of strain N6 grown on protocatechuate or 4-hydroxybenzoic acid mainly protocatechuate 3,4-dioxygenase was induced. The activity of catechol 1,2-dioxygenase was rather small. The cells grown on benzoic acid, catechol or phenol showed high activity of only catechol 1,2-dioxygenase. This enzyme was optimally active at 35°C and pH 7.4. Kinetic studies showed that the value of Km and Vmax was 85.19μM and 14.54μMmin-1 respectively. Nucleotide sequence of gene encoding catechol 1,2-dioxygenase in strain N6 has 100% identity with catA genes from two P. putida strains. The deduced 301-residue sequence of enzyme corresponds to a protein of molecular mass 33.1kDa. The deduced molecular structure of the catechol 1,2-dioxygenase from P. putida N6 was very similar and characteristic for the other intradiol dioxygenases. © 2011 Elsevier Ltd.},

note = {45},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-79952572933,

title = {Induction of aromatic ring: Cleavage dioxygenases in Stenotrophomonas maltophilia strain KB2 in cometabolic systems},

author = { D. Wojcieszyńska and U. Guzik and I. Greń and M. Perkosz and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79952572933&doi=10.1007%2fs11274-010-0520-6&partnerID=40&md5=c1266ef2c54e06fa02156c466ae15eed},

doi = {10.1007/s11274-010-0520-6},

issn = {09593993},

year  = {2011},

date = {2011-01-01},

journal = {World Journal of Microbiology and Biotechnology},

volume = {27},

number = {4},

pages = {805-811},

abstract = {Stenotrophomonas maltophilia KB2 is known to produce different enzymes of dioxygenase family. The aim of our studies was to determine activity of these enzymes after induction by benzoic acids in cometabolic systems with nitrophenols. We have shown that under cometabolic conditions KB2 strain degraded 0.25-0.4 mM of nitrophenols after 14 days of incubation. Simultaneously degradation of 3 mM of growth substrate during 1-3 days was observed depending on substrate as well as cometabolite used. From cometabolic systems with nitrophenols as cometabolites and 3,4-dihydroxybenzoate as a growth substrate, dioxygenases with the highest activity of protocatechuate 3,4-dioxygenase were isolated. Activity of catechol 1,2- dioxygenase and protocatechuate 4,5-dioxygenase was not observed. Catechol 2,3-dioxygenase was active only in cultures with 4-nitrophenol. Ability of KB2 strain to induce and synthesize various dioxygenases depending on substrate present in medium makes this strain useful in bioremediation of sites contaminated with different aromatic compounds. © 2010 The Author(s).},

note = {48},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-81355139502,

title = {Modulation of FAD-dependent monooxygenase activity from aromatic compounds-degrading Stenotrophomonas maltophilia strain KB2},

author = { D. Wojcieszyńska and I. Greń and K.T. Hupert-Kocurek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-81355139502&doi=10.18388%2fabp.2011_2256&partnerID=40&md5=cf851e7c3fa3a0bbc0603a8971168364},

doi = {10.18388/abp.2011_2256},

issn = {0001527X},

year  = {2011},

date = {2011-01-01},

journal = {Acta Biochimica Polonica},

volume = {58},

number = {3},

pages = {421-426},

publisher = {Acta Biochimica Polonica},

abstract = {The purpose of this study was purification and characterization of phenol monooxygenase from Stenotrophomonas maltophilia strain KB2, enzyme that catabolises phenol and its derivatives through the initial hydroxylation to catechols. The enzyme requires NADH and FAD as a cofactors for activity, catalyses hydroxylation of a wide range of monocyclic phenols, aromatic acids and dihydroxylated derivatives of benzene except for catechol. High activity of this monooxygenase was observed in cell extract of strain KB2 grown on phenol, 2-methylphenol, 3-metylphenol or 4-methylphenol. Ionic surfactants as well as cytochrome P450 inhibitors or 1,4-dioxane, acetone and n-butyl acetate inhibited the enzyme activity, while non-ionic surfactants, chloroethane, ethylbenzene, ethyl acetate, cyclohexane, and benzene enhanced it. These results indicate that the phenol monooxygenase from Stenotrophomonas maltophilia strain KB2 holds great potential for bioremediation.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84862875187,

title = {Activity of catechol dioxygenases in the presence of some heavy metal ions: Bioremediation of an environment polluted with aromatic compounds [Badania aktywności dioksygenaz katecholowych w obecności jonów wybranych metali ciȩżkich w aspekcie bioremediacji środowisk zanieczyszczonych zwia̧zkami aromatycznymi]},

author = { U. Guzik and D. Wojcieszyńska and I. Greń and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84862875187&partnerID=40&md5=86313da0b90e3633bb0a7ddecc001794},

issn = {12306169},

year  = {2010},

date = {2010-01-01},

journal = {Ochrona Srodowiska},

volume = {32},

number = {1},

pages = {9-13},

abstract = {The strains of Stenotrophomonas maltophilia KB2 and Pseudomonas putida N6 are characterized by an enhanced capacity for degrading aromatic compounds: within five hours of incubation both the strains were found to provide a complete degradation of phenol (3 mmol/dm3). Upon induction with phenol, catechol 2,3-dioxygenase, an enzyme responsible for the meta-cleavage of aromatic compounds, was detected in the Stenotrophomonas maltophilia KB2 strain, whereas in the Pseudomonas putida N6 strain the presence was revealed of catechol 1,2-dioxygenase, an enzyme characteristic of the pathway for the ortho-fission of the aromatic ring. Tests on the sensitivity of the enzymes to metal ions have demonstrated that Zn 2+ ions activated catechol 2,3-dioxygenase in the KB2 strain. The other metal ions were found to be inhibitors of this enzyme. Among the metal ions tested, the Cu 2+ ion was the strongest inhibitor of the two isolated dioxynases. Slightly weaker was the inhibition of catechol 1,2-dioxygenase induced by Cd 2+ and Zn 2+ ions in the N6 strain. The activity of this enzyme increased in the presence of Co 2+ ions. The other ions had no significant influence on the activity of the catechol 1,2-dioxygenase isolated from the N6 strain. The partial activity of both dioxygenases observed upon the application of metal salts suggests that both the strains, Stenotrophomonas maltophilia KB2 and Pseudomonas putida N6, may contribute much to the remediation of an environment polluted with aromatic compounds.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-77951141722,

title = {Enhanced biotransformation of mononitrophenols by Stenotrophomonas maltophilia KB2 in the presence of aromatic compounds of plant origin},

author = { I. Greń and D. Wojcieszyńska and U. Guzik and M. Perkosz and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77951141722&doi=10.1007%2fs11274-009-0172-6&partnerID=40&md5=10c990c0b3a65918797b592059052a18},

doi = {10.1007/s11274-009-0172-6},

issn = {09593993},

year  = {2010},

date = {2010-01-01},

journal = {World Journal of Microbiology and Biotechnology},

volume = {26},

number = {2},

pages = {289-295},

abstract = {Stenotrophomonas maltophilia KB2 used in this study is known to metabolise broad range of aromatic compounds including phenol, some chloro and methylphenols, benzoic acids, catochols and others. To study the applicability of the strain for degradation of mononitrophenols in monosubstrate as well as cometabolic systems its degradation potential in the presence of mononitrophenols or different aromatic compounds of plant origin was tested. Stenotrophomonas maltophilia KB2 strain was not able to degrade any of mononitrophenols used in the single substrate experiments. Effect of additional carbon source on nitrophenols degradation revealed that presence of benzoate, 4-hydroxybenzoate or 3,4-dixydroxybenzoate stimulate transformation of 2-nitrophenol, 3-nitrophenol as well as 4-nitrophenol. Depending on growth substrate and mononitrophenol used, decrease in cometabolite concentration was from 25 to 45%. Obtained results suggest that Stenotrophomonas maltophilia KB2 strain could be potentially used for cometabolic degradation of nitrophenols in the presence of aromatic acids, for the bioremediation of contaminated sites. © 2009 Springer Science+Business Media B.V.},

note = {49},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-44349151101,

title = {Microbial lipases and their significance in the protection of the environment},

author = { A. Mrozik and K.T. Hupert-Kocurek and B. Nowak and S. Łabuzek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-44349151101&partnerID=40&md5=f89c74471d08508902cd4b99ba6cc9cc},

issn = {00794252},

year  = {2008},

date = {2008-01-01},

journal = {Postepy Mikrobiologii},

volume = {47},

number = {1},

pages = {43-50},

abstract = {Microbial lipases represent an extremely versatile group of enzymes that are capable of performing a variety of important reactions. They belong to the class of serine hydrolases and act at the interface generated by a hydrophobic lipid substrate in a hydrophilic medium. Their synthesis and secretion by microorganisms is influenced by many factors like temperature, pH, ions, carbon and nitrogen sources and dissolved oxygen concentration. Microbial lipases are used in leather, detergent, pulp and paper industry, sewage treatment, biodiesel and biodegradable polymers production and bioremediation. Due to various properties lipases are helpful tools in biotechnology and environment protection fields.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-35949003233,

title = {Genetic method to analyze essential genes of Escherichia coli},

author = { K.T. Hupert-Kocurek and J.M. Sage and M. Makowska-Grzyska and J.M. Kaguni},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-35949003233&doi=10.1128%2fAEM.01756-07&partnerID=40&md5=6832cbd7330c06f16ceaad709ed7bc08},

doi = {10.1128/AEM.01756-07},

issn = {00992240},

year  = {2007},

date = {2007-01-01},

journal = {Applied and Environmental Microbiology},

volume = {73},

number = {21},

pages = {7075-7082},

abstract = {The genetic analysis of essential genes has been generally restricted to the use of conditional mutations, or inactivating chromosomal mutations, which require a complementing plasmid that must either be counter-selected or lost to measure a phenotype. These approaches are limited because they do not permit the analysis of mutations suspected to affect a specific function of a protein, nor do they take advantage of the increasing abundance of structural and bioinformatics data for proteins. Using the dnaC gene as an example, we developed a genetic method that should permit the mutational analysis of other essential genes of Escherichia coli and related enterobacteria. The method consists of using a strain carrying a large deletion of the dnaC gene, which is complemented by a wild-type copy expressed from a plasmid that requires isopropyl-β-D-thiogalactopyranoside for maintenance. Under conditions in which this resident plasmid is lost, the method measures the function of a dnaC mutation encoded by a second plasmid. This methodology should be widely applicable to the genetic analysis of other essential genes. Copyright © 2007, American Society for Microbiology. All Rights Reserved.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-33745941602,

title = {Regulatory proteins in control of aromatic compounds degradation in Pseudomonas [Białka regulatorowe w kontroli ekspresji genów degradacji zwia̧zków o strukturze aromatycznej u bakterii rodzaju Pseudomonas]},

author = { K.T. Hupert-Kocurek and A. Mrozik and S. Łabuzek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33745941602&partnerID=40&md5=91dc1da6b2bd2ef5b8680f2d24a93f97},

issn = {00794252},

year  = {2006},

date = {2006-01-01},

journal = {Postepy Mikrobiologii},

volume = {45},

number = {2},

pages = {97-106},

abstract = {A number of degradative pathways of aromatic compounds, such as phenol, toluene xylene and naphthalene, have been found in many strains of genus Pseudomonas. The expression of these degradative genes is controlled by one or more regulatory proteins. In most cases, the genes coding for the regulator exist near the structural genes, and their protein products activate the transcription in the presence of inducer molecule. Repressor-mediated regulation is rare for genes involved in the catabolism of aromatic compounds. According to differences in structure, three-demensional conformation and mechanism of regulation, all regulatory proteins are divided into seven families: LysR, IclR, AraC/XylS, GntR families, TetR-, MarR-type regulators, XylR/DmpR σ54-dependent transcriptional regulators and two-component regulatory system. In general, there are two functional domains in regulatory protein structure. The domain containing the HTH DNA binding motif in regulators from LysR, IclR and GntR family is located at N-terminal end of the polipeptyde. The second one, C-terminal domain is involved in binding of the chemical inducer and oligomerization. Some of regulatory proteins, especially from XylR/DmpR family, posess the third domain, which is responsible for ATP binding and hydrolysis. Most of identified regulatory proteins which control aromatic degradation pathways bound DNA in specific region called RBS, except LysR type regulators which recognize additional sequence known as ABS. All regulators are synthesized as non-active monomers. In the presence of inducer they oligomerize to dimers, tetramers, hexamers or heptamers depending of family. As a result of many studies the behavior of different regulatory proteins was discovered. In some cases it has been possible to identify the protein structure, protein-DNA complex formation and conformational changes in regulators after effector binding. In contrast, little is currently known about the interactions between the regulatory protein and effector compounds and how effector binding to the regulatory protein transmits to an activation signal for RNA polymerase. The understanding of these interactions might be an important challenge for the application of bacterial regulatory systems for bioremediation practice, chemical synthesis and as biosensors for measuring the quality of soil and waters.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-33745317192,

title = {Lipases of genera Pseudomonas and Burkholderia and their applications in biotechnology [Lipazy bakterii rodzajów pseudomonas i burkholderia oraz ich wykorzystanie w biotechnologii]},

author = { A. Mrozik and K.T. Hupert-Kocurek and S. Łabuzek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33745317192&partnerID=40&md5=7697b5c43f5b23f7fa7e6cfde40029a0},

issn = {00794252},

year  = {2006},

date = {2006-01-01},

journal = {Postepy Mikrobiologii},

volume = {45},

number = {1},

pages = {19-26},

abstract = {Lipases (triacylglycerol acylhydrolases; EC 3.1.1.3) catalyze the hydrolysis and trans-esterification of triglycerides, enantioselective synthesis, and the hydrolysis of a variety of esters. According to their substrate specificity lipases are divided into three groups. The first group contains lipases showing no positional and no specificity to the chemical structure of fatty acid. Lipases of the second group hydrolyze only primary ester bonds while those of the third group exhibit a pronounced fatty acid preference. Lipases, in contrast to esterases, are activated only when absorbed to an oil-water interface and do not hydrolyze dissolved substrates in the bulk fluid. They are produce by many strains of bacteria, especially of the genus Pseudomonas, Burkholderia, Acinetobacter and Staphylococcus, and fungi, for example Aspergillus terreus and Fusarium heterosporum. Microbial lipases have molecular weight of 19-60 kDa and are produced in the end of logarytmic phase of growth. All enzymes exhibit a characteristic folding pattern known as the α/β-hydrolyze fold. Their active-site is composed of the catalytic triad serine, histidine and an acid residue, Asp or Glu. Based on sequence of aminoacid, Pseudomonas and Burkholderia lipases were classified into three families. Lipases from families I and II show more similarities, whereas family III lipases are larger (50 kDa) and untrelated to the other lipases. All known bacterial lipases are extracellular enzymes requiring their translocation through the inner and outer membranes. Lipases of Pseudomonas are secreted by two types of secretion pathways: ABC exporters and general secretary pathway (GSP). Efficient secretion of lipases is coupled to correct folding. This process involves specific foldase and unspecific Dsb-proteins. Because of their wide-ranging significance, lipases remain a subject of intensive studies. Researches of lipases are focused particularly on structural characterization, elucidation of mechanism of action, kinetics, sequencing and cloning of lipase genes, folding and secrection. Lipases find promising applications in organic chemical processing, detergent production, synthesis of biosurfactants, the oleochemical industry, the dairy industry, the agrochemical activity, paper manufacture, nutrition, cosmetics and pharmaceutical processing.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0742288464,

title = {Isolation and Characterisation of New Planococcus sp. Strain Able for Aromatic Hydrocarbons Degradation},

author = { S. Łabuzek and K.T. Hupert-Kocurek and M. Skurnik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0742288464&partnerID=40&md5=b2eb0dbb0f5254cc39e2725ae2fe2a9a},

issn = {01371320},

year  = {2003},

date = {2003-01-01},

journal = {Acta Microbiologica Polonica},

volume = {52},

number = {4},

pages = {395-404},

abstract = {New Planococcus sp. strain S5 able to grow on salicylate or benzoate as sole carbon source was isolated from activated sludge adapted to sodium salicylate degradation. S5 was determined to be a strictly aerobic, gram-positive, catalase positive, oxidase negative, non-motile, non-spore forming coccus. The strain harboured a plasmid, named pLS5. The S5 strain when grown on salicylate expressed both catechol 1,2-dioxygenase and catechol 2,3-dioxygenase activities and degraded this substrate by both the ortho and meta pathways while grown on benzoate expressed only catechol 1,2-dioxygenase activity. Curing of the plasmid from the strain showed that plasmid pLS5 was involved in salicylate degradation by the meta pathway.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}