The organization of naphthalene degradation genes in Pseudomonas putida strain AK5

Izmalkova, T. Yu.; Сазонова, О. И.; Nagornih, Maxim O.; Sokolov, S. L.; Кошелева, И. А.; Boronin, A. M.

doi:10.1016/j.resmic.2012.12.007

Cited by 45 publications

(27 citation statements)

References 36 publications

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“…Despite these properties, a variety of bacterial species can degrade PAHs. Most research on the enzymes involved in PAH metabolism and genetic regulation is focused on Pseudomonas and Sphingomonas species [6]–[11], but Mycobacterium , Rhodococcus , Nocardioides , and Novosphingobium species can also mineralize PAHs [12], [13]. Proposed pathways for pyrene biodegradation by mycobacteria have been reported [14], including the complete pathway to the tricarboxylic acid (TCA) cycle proposed for Mycobacterium vanbaalenii PYR-1, but little is known about the genetic and enzymatic processes involved in the PAHs degradative pathways used by Novosphingobium species.…”

Section: Introductionmentioning

confidence: 99%

Biodegradation of Polycyclic Aromatic Hydrocarbons by Novosphingobium pentaromativorans US6-1

Yihua

Zheng

et al. 2014

PLoS ONE

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Novosphingobium pentaromativorans US6-1, a marine bacterium isolated from muddy sediments of Ulsan Bay, Republic of Korea, was previously shown to be capable of degrading multiple polycyclic aromatic hydrocarbons (PAHs). In order to gain insight into the characteristics of PAHs degradation, a proteome analysis of N. pentaromativorans US6-1 exposed to phenanthrene, pyrene, and benzo[a]pyrene was conducted. Several enzymes associated with PAHs degradation were identified, including 4-hydroxybenzoate 3-monooxygenase, salicylaldehyde dehydrogenase, and PAH ring-hydroxylating dioxygenase alpha subunit. Reverse transcription and real-time quantitative PCR was used to compare RHDα and 4-hydroxybenzoate 3-monooxygenase gene expression, and showed that the genes involved in the production of these two enzymes were upregulated to varying degrees after exposing the bacterium to PAHs. These results suggested that N. pentaromativorans US6-1 degraded PAHs via the metabolic route initiated by ring-hydroxylating dioxygenase, and further degradation occurred via the o-phthalate pathway or salicylate pathway. Both pathways subsequently entered the tricarboxylic acid (TCA) cycle, and were mineralized to CO2.

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Section: Introductionmentioning

confidence: 99%

Biodegradation of Polycyclic Aromatic Hydrocarbons by Novosphingobium pentaromativorans US6-1

Yihua

Zheng

et al. 2014

PLoS ONE

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“…This growth was limited with the M. radiotolerans strain but was very high with P. aeruginosa (Table 1), thus the latter strain can effi ciently express catabolic enzymes of the "salicylate pathway". The existence of this pathway has already been proven in P. aeruginosa (Civilini et al 1999, Takizawa et al 1999, and in other bacteria of the genus Pseudomonas (Izmalkova et al 2013, Phale et al 2013. The growth of M. radiotolerans in the presence of salicylic acid or catechol is lower than in the presence of naphthalene, yet one would have expected these single ring molecules to be easily catabolised, thus supporting a higher bacteria growth.…”

Section: Detection Of Metabolites By Gc-msmentioning

confidence: 93%

“…The second pathway has been studied the most, and genes encoding for these catabolic enzymes are generally found in bacterial extra-chromosome plasmids, and plasmids from several bacterial species have been A. Nzila, A. Thukair, S. Sankara, B. Chanbasha, M.M. Musa characterized, including the plasmid NAH7 of Pseudomonas putida strain G (Fernandez et al 2012), pAK5 of Pseudomonas putida strain AK5 (Izmalkova et al 2013), and plasmid of Gordonia sp. strain CC-NAPH129-6 (Izmalkova et al 2013).…”

Section: Detection Of Metabolites By Gc-msmentioning

confidence: 99%

“…Musa characterized, including the plasmid NAH7 of Pseudomonas putida strain G (Fernandez et al 2012), pAK5 of Pseudomonas putida strain AK5 (Izmalkova et al 2013), and plasmid of Gordonia sp. strain CC-NAPH129-6 (Izmalkova et al 2013). The analysis showed a GC peak at a retention time of 14.1 min ( Figure S1, S3), with a molecular mass of 132, and fragmentation pattern ( Figure S2a) consistent with 4-hydroxy-2-oxovaleric acid, a metabolite in the catechol pathway (Figure 1; Table 2).…”

Section: Detection Of Metabolites By Gc-msmentioning

confidence: 99%

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Isolation and characterization of naphthalene biodegrading Methylobacterium radiotolerans bacterium from the eastern coastline of the Kingdom of Saudi Arabia

Nzila¹,

Thukair²,

Sankara³

et al. 2016

Archives of Environmental Protection

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Bioremediation is based on microorganisms able to use pollutants either as a source of carbon or in co-metabolism, and is a promising strategy in cleaning the environment. Using soil contaminated with petroleum products from an industrial area in Saudi Arabia (Jubail), and after enrichment with the polycyclic aromatic hydrocarbon (PAH) naphthalene, a Methylobacterium radiotolerans strain (N7A0) was isolated that can grow in the presence of naphthalene as the sole source of carbon. M. radiotolerans is known to be resistant to gamma radiation, and this is the fi rst documented report of a strain of this bacterium using a PAH as the sole source of carbon. The commonly reported Pseudomonas aeruginosa (strain N7B1) that biodegrades naphthalene was also identifi ed, and gas chromatography analyses have shown that the biodegradation of naphthalene by M. radiotolerans and P. aeruginosa did follow both the salicylate and phthalate pathways.

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“…The aromatic-inducible SIGEX clones are inducible to different extents by a given chemical, and individual clones also show specific patterns of expression in the presence of different chemicals (Figure 4.5 from Pseudomonas putida (GenBank accession FJ859895; Izmalkova et al, 2013).…”

Section: Determining Biological Roles For Sequences Surrounding Sigexmentioning

confidence: 99%

Metagenomic Analysis of Contaminated Soils

Meier¹

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Several metagenomic techniques were applied to analyze the microbial communities found in contaminated sites. A high-throughput metagenomic method called substrate-induced gene expression (SIGEX) was used to screen for genes that were upregulated by xenobiotic pollutants within a metagenomic library.SIGEX uses a promoterless green fluorescent protein (GFP) as a reporter for the transcription of metagenomic DNA that has been cloned in a plasmid library.Through propagation of metagenomic libraries in liquid culture, we used flow cytometry and fluorescence-activated cell-sorting to sort and analyze rare clones with desired expression characteristics. Using microbial DNA isolated from a polycyclic aromatic-contaminated site, clones that were inducible by a variety of aromatic hydrocarbons were recovered using SIGEX. These inducible elements were examined for sequence similarity to known genes, and were found to contain different types of aromatic-metabolizing oxygenases and efflux pumps, along with their respective regulatory genes. Most often, the sequences were those of partial operons containing various nahG (salicylate oxygenase) family genes, along with their respective upstream nahR regulators. Next-generation sequencing was used to map these small plasmid-based clones (representing relatively small fragments of the metagenome, on the order of 1 to 5 kilobases) to larger contigs (up to 61 kilobases) derived from the de novo assembly of 125 gigabases of shotgunsequenced metagenomic DNA. These contigs were annotated using a variety of gene and protein prediction tools and were found to contain entire operons related iii to aromatic hydrocarbon metabolism; this enabled a more complete functional and taxonomic assignment of the sequences recovered through SIGEX analysis. To assess the presence of relevant gene classes that were not recovered with SIGEX, genes with the capacity for xenobiotic metabolism were screened in silico within the assembled metagenomic reads using the biodegradation gene database and MG-RAST annotation. The taxonomic relationships between these functional genes were evaluated. As a direct application of this work, we show that SIGEX can be used to aid in the discovery and design of novel whole-cell bioreporters for the detection of xenobiotics.iv AcknowledgementsThe research presented in this thesis was possible only because of the incredible help I have received throughout the course of my studies.First and foremost, I would like to thank my supervisor -Dr. Iain Lambertwho has taught me more about doing science the correct way than any textbook or journal article ever could. His enthusiasm and curiosity are a huge asset to all the students he mentors, and his support over the years (in many capacities) has been tremendous.Within the Carleton and Ottawa Biology faculty there are many individuals I would like to thank who have provided assistance (in the form of teaching, advice, access to equipment/chemicals, and occasionally beer), including Drs. Myron

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The organization of naphthalene degradation genes in Pseudomonas putida strain AK5

Cited by 45 publications

References 36 publications

Biodegradation of Polycyclic Aromatic Hydrocarbons by Novosphingobium pentaromativorans US6-1

Biodegradation of Polycyclic Aromatic Hydrocarbons by Novosphingobium pentaromativorans US6-1

Isolation and characterization of naphthalene biodegrading Methylobacterium radiotolerans bacterium from the eastern coastline of the Kingdom of Saudi Arabia

Metagenomic Analysis of Contaminated Soils

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