-
Genomics Data Dec 2017. DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace...
. DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70 tRNA loci. In addition, approximately 142 proteins localized on the bacterial chromosome are associated with metabolism of aromatic compounds. A single plasmid approximately 95 kb in size was also detected carrying copies of RNA genes and multiple phage assembly proteins.
PubMed: 28856100
DOI: 10.1016/j.gdata.2017.07.011 -
Applied Microbiology and Biotechnology Jun 2017The surfactant sodium lauryl ether sulfate (SLES) is widely used in the composition of detergents and frequently ends up in wastewater treatment plants (WWTPs). While...
The surfactant sodium lauryl ether sulfate (SLES) is widely used in the composition of detergents and frequently ends up in wastewater treatment plants (WWTPs). While aerobic SLES degradation is well studied, little is known about the fate of this compound in anoxic environments, such as denitrification tanks of WWTPs, nor about the bacteria involved in the anoxic biodegradation. Here, we used SLES as sole carbon and energy source, at concentrations ranging from 50 to 1000 mg L, to enrich and isolate nitrate-reducing bacteria from activated sludge of a WWTP with the anaerobic-anoxic-oxic (A/O) concept. In the 50 mg L enrichment, Comamonas (50%), Pseudomonas (24%), and Alicycliphilus (12%) were present at higher relative abundance, while Pseudomonas (53%) became dominant in the 1000 mg L enrichment. Aeromonas hydrophila strain S7, Pseudomonas stutzeri strain S8, and Pseudomonas nitroreducens strain S11 were isolated from the enriched cultures. Under denitrifying conditions, strains S8 and S11 degraded 500 mg L SLES in less than 1 day, while strain S7 required more than 6 days. Strains S8 and S11 also showed a remarkable resistance to SLES, being able to grow and reduce nitrate with SLES concentrations up to 40 g L. Strain S11 turned out to be the best anoxic SLES degrader, degrading up to 41% of 500 mg L. The comparison between SLES anoxic and oxic degradation by strain S11 revealed differences in SLES cleavage, degradation, and sulfate accumulation; both ester and ether cleavage were probably employed in SLES anoxic degradation by strain S11.
Topics: Aeromonas; Biodegradation, Environmental; Carbon; Comamonadaceae; Comamonas; Denitrification; Gram-Negative Bacteria; Oxidation-Reduction; Pseudomonas; Sewage; Sodium Dodecyl Sulfate; Surface-Active Agents
PubMed: 28299401
DOI: 10.1007/s00253-017-8212-x -
Applied and Environmental Microbiology Nov 2016Pseudomonas nitroreducens TX1 is of special interest because of its ability to utilize 0.05% to 20% octylphenol polyethoxylates (OPEO) as a sole source of carbon. In...
Pseudomonas nitroreducens TX1 is of special interest because of its ability to utilize 0.05% to 20% octylphenol polyethoxylates (OPEO) as a sole source of carbon. In this study, a library containing 30,000 Tn5-insertion mutants of the wild-type strain TX1 was constructed and screened for OPEO utilization, and 93 mutants were found to be unable to grow on OPEO In total, 42 separate disrupted genes were identified, and the proteins encoded by the genes were then classified into various categories, namely, information storage and processing (14.3%), cellular processes and signaling (28.6%), metabolism (35.7%), and unknown proteins (21.4%). The individual deletion of genes encoding isocitrate lyase (aceA), malate synthase (aceB), and glycolate dehydrogenase (glcE) was carried out, and the requirement for aceA and aceB but not glcE confirmed the role of the glyoxylate cycle in OPEO degradation. Furthermore, acetaldehyde dehydrogenase and acetyl-coenzyme A (acetyl-CoA) synthetase activity levels were 13.2- and 2.1-fold higher in TX1 cells grown on OPEO than in TX1 cells grown on succinate, respectively. Growth of the various mutants on different carbon sources was tested, and based on these findings, a mechanism involving exoscission to liberate acetaldehyde from the end of the OPEO chain during degradation is proposed for the breakdown of OPEO IMPORTANCE: Octylphenol polyethoxylates belong to the alkylphenol polyethoxylate (APEO) nonionic surfactant family. Evidence based on the analysis of intermediate metabolites suggested that the primary biodegradation of APEO can be achieved by two possible pathways for the stepwise removal of the C ethoxylate units from the end of the chain. However, direct evidence for these hypotheses is still lacking. In this study, we described the use of transposon mutagenesis to identify genes critical to the catabolism of OPEO by P. nitroreducens TX1. The exoscission of the ethoxylate chain leading to the liberation of acetaldehyde is proposed. Isocitrate lyase and malate synthase in glyoxylate cycle are required in the catabolism of ethoxylated surfactants. Our findings also provide many gene candidates that may help elucidate the mechanisms in stress responses to ethoxylated surfactants by bacteria.
Topics: Acetaldehyde; Alcohol Oxidoreductases; Aldehyde Oxidoreductases; Bacterial Proteins; DNA Transposable Elements; Gene Deletion; Isocitrate Lyase; Malate Synthase; Mutagenesis, Insertional; Phenols; Pseudomonas; Succinic Acid; Surface-Active Agents
PubMed: 27590807
DOI: 10.1128/AEM.01907-16 -
Pyrimidine nucleotide synthesis in Pseudomonas nitroreducens and the regulatory role of pyrimidines.Microbiological Research Dec 2014Control of pyrimidine biosynthesis in the commercially important, hydrocarbon-utilizing bacterium Pseudomonas nitroreducens ATCC 33634 was investigated. When...
Control of pyrimidine biosynthesis in the commercially important, hydrocarbon-utilizing bacterium Pseudomonas nitroreducens ATCC 33634 was investigated. When glucose-grown wild-type cells were supplemented with uracil or orotic acid, the pyrimidine biosynthetic activities were depressed. Pyrimidine limitation of glucose-grown cells of an orotate phosphoribosyltransferase mutant caused aspartate transcarbamoylase and dihydroorotase activities to increase by about 4-fold while the other enzyme activities about doubled. In succinate-grown phosphoribosyltransferase mutant cells subjected to pyrimidine limitation, transcarbamoylase and dehydrogenase activities rose by about 5-fold while dihydroorotase activity more than tripled. In an OMP decarboxylase mutant, pyrimidine limitation of glucose-grown cells increased transcarbamoylase, dihydroorotase, dehydrogenase and phosphoribosyltransferase activities by 4-, 10-, 6- and 3.8-fold, respectively. Pyrimidine limitation of the succinate-grown decarboxylase mutant cells increased aspartate transcarbamoylase or dihydroorotase by more than 4-fold and the other activities by about 2-fold. Pyrimidine biosynthetic enzyme synthesis appeared to be regulated by pyrimidines with the regulation being influenced by the carbon source present. Aspartate transcarbamoylase activity in Ps. nitroreducens was regulated at the level of enzyme activity since the enzyme was strongly inhibited by UDP, pyrophosphate, ATP and ADP. Overall, the regulation of pyrimidine biosynthesis in Ps. nitroreducens can be used to differentiate it from other taxonomically related species of Pseudomonas.
Topics: Aspartate Carbamoyltransferase; Pseudomonas; Pyrimidine Nucleotides; Pyrimidines
PubMed: 24867376
DOI: 10.1016/j.micres.2014.04.003 -
Genome Announcements Jan 2014Pseudomonas nitroreducens TX1 ATCC PTA-6168 was isolated from rice field drainage in Taiwan. The bacterium is of special interest because of its capability to use...
Pseudomonas nitroreducens TX1 ATCC PTA-6168 was isolated from rice field drainage in Taiwan. The bacterium is of special interest because of its capability to use nonionic surfactants (alkylphenol polyethoxylates) and estrogen-like compounds (4-t-octylphenol and 4-nonylphenol) as a sole carbon source. This is the first report on the genome sequence of P. nitroreducens.
PubMed: 24482523
DOI: 10.1128/genomeA.01262-13 -
BMC Microbiology Mar 2013The agrichemical 4-aminopyridine is used as a bird repellent in crop fields and has an epileptogenic action in a variety of animals, including man and mouse....
BACKGROUND
The agrichemical 4-aminopyridine is used as a bird repellent in crop fields and has an epileptogenic action in a variety of animals, including man and mouse. 4-Aminopyridine is biodegraded in the environment through an unknown mechanism.
RESULTS
A 4-aminopyridine-degrading enrichment culture utilized 4-aminopyridine as a carbon, nitrogen, and energy source, generating 4-amino-3-hydroxypyridine, 3,4-dihydroxypyridine, and formate as intermediates. 4-Amino-3-hydroxypyridine could not be further metabolized and probably accumulated as a dead-end product in the culture. Biodegradability tests and partial sequence analysis of the enrichment culture indicated that 4-aminopyridine was mainly degraded via 3,4-dihydroxypyridine and that the metabolite is probably cleaved by 3-hydroxy-4-pyridone dioxygenase. Seven culturable predominant bacterial strains (strains 4AP-A to 4AP-G) were isolated on nutrient agar plates. Changes in the bacterial populations of 4-aminopyridine, 3,4-dihydroxypyridine, or formate/ammonium chloride enrichment cultures were monitored by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Sequence analysis of the 16S rRNA gene fragments derived from predominant DGGE bands indicated that Pseudomonas nitroreducens 4AP-A and Enterobacter sp. 4AP-G were predominant in the three tested enrichment cultures and that the unculturable strains Hyphomicrobium sp. 4AP-Y and Elizabethkingia sp. 4AP-Z were predominant in 4-aminopyridine and formate/ammonium chloride enrichment cultures and in the 3,4-dihydroxypyridine enrichment culture, respectively. Among the culturable strains, strain 4AP-A could utilize 3,4-dihydroxypyridine as a growth substrate. Although we could not isolate strain 4AP-Y on several media, PCR-DGGE analysis and microscopy indicated that the unique bi-polar filamentous bacterial cells gradually became more dominant with increasing 4-aminopyridine concentration in the medium.
CONCLUSIONS
Hyphomicrobium sp. 4AP-Y, P. nitroreducens 4AP-A, and Elizabethkingia sp. 4AP-Z probably play important roles in 4-aminopyridine degradation in crop fields. In the enrichment culture, 3,4-dihydroxypyridine and its metabolites including formate might be shared as growth substrates and maintain the enrichment culture, including these indispensable strains.
Topics: 4-Aminopyridine; Bacteria; Biota; Biotransformation; DNA, Bacterial; DNA, Ribosomal; Environmental Pollutants; Molecular Sequence Data; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology
PubMed: 23517195
DOI: 10.1186/1471-2180-13-62 -
Bioscience, Biotechnology, and... 2013The isoeugenol monooxygenase (iem) gene from Pseudomonas nitroreducens Jin1, responsible for the conversion of isoeugenol to vanillin, was cloned and overexpressed in...
The isoeugenol monooxygenase (iem) gene from Pseudomonas nitroreducens Jin1, responsible for the conversion of isoeugenol to vanillin, was cloned and overexpressed in Escherichia coli. The purified Iem had a predicted molecular mass of 54 kDa. The V(max), K(M), and k(cat) values for it, using isoeugenol as substrate, were 4.2 µmol vanillin min(-1) mg(-1) of protein, 120 µM, and 3.8 s(-1), respectively. Maximum substrate turnover for Iem occurred at 30 °C and pH 9.0. An (18)Oxygen-labeling experiment revealed that oxidative cleavage of isoeugenol by Iem was catalyzed via a monooxygenation reaction, and that incorporation of the oxygen atom from O(2) into vanillin was preferable to incorporation from water. While the catalytic activity of Iem, as prepared, did not require the addition of any organic or metal cofactor, ICP-MS analysis showed 0.7 mol of iron per mol of Iem. Moreover site-directed mutagenesis of Iem of four conserved histidine residues individually, His(167), His(218), His(282), and His(471), which appear to be involved in ligand bonding with Fe(2+), resulted in a loss of activity. Enzyme activity was not appreciably influenced by preincubation of Iem with high concentrations of chelators, suggesting that iron is tightly bound. Iem has an iron-mediated mechanism that is widely spread among the three domains of life.
Topics: Bacterial Proteins; Benzaldehydes; Biotransformation; Cloning, Molecular; Escherichia coli; Eugenol; Gene Expression; Histidine; Hydrogen-Ion Concentration; Iron; Iron Chelating Agents; Kinetics; Mixed Function Oxygenases; Molecular Weight; Mutagenesis, Site-Directed; Oxygen; Oxygen Isotopes; Pseudomonas; Recombinant Proteins
PubMed: 23391906
DOI: 10.1271/bbb.120715 -
Bioscience, Biotechnology, and... 2012Vanillin is one of the most valuable compounds in the flavoring and fragrance industries, and many attempts to produce natural vanillin have been made in recent years....
Vanillin is one of the most valuable compounds in the flavoring and fragrance industries, and many attempts to produce natural vanillin have been made in recent years. Isoeugenol monooxygenase (Iem) converts the phenylpropanoid compound isoeugenol to vanillin. In Pseudomonas nitroreducens Jin1, the positive regulatory protein IemR is divergently expressed from Iem, and the promoter region is located between the genes. In this study, we investigated the transcriptional regulation of iem in Escherichia coli. We focused on inducers and regulatory protein IemR. Transcription of iem was found to be dependent on the amounts of isoeugenol and IemR. Isoeugenol was found to be the best inducer of iem, followed by trans-anethole, which induced iem to 58% of the transcription level observed for isoeugenol. Overproduction of IemR in E. coli significantly increased the transcription of iem, up to 96-fold, even in the absence of isoeugenol, as compared to basally expressed IemR. Results of this study indicate that the transcription of iem iss dependent on the type of inducers and on IemR. They should contribute to the development of bioengineering strategies for increased production of vanillin through high-level expression of the isoeugenol monooxygenase gene in microorganisms.
Topics: Bacterial Proteins; Base Sequence; Escherichia coli; Eugenol; Gene Expression Regulation, Bacterial; Mixed Function Oxygenases; Molecular Sequence Data; Pseudomonas; Transcription, Genetic
PubMed: 23047101
DOI: 10.1271/bbb.120375 -
Applied and Environmental Microbiology Aug 2012A plasmid, pTA163, in Escherichia coli contained an approximately 34-kb gene fragment from Pseudomonas putida JYR-1 that included the genes responsible for the...
A plasmid, pTA163, in Escherichia coli contained an approximately 34-kb gene fragment from Pseudomonas putida JYR-1 that included the genes responsible for the metabolism of trans-anethole to protocatechuic acid. Three Tn5-disrupted open reading frame 10 (ORF 10) mutants of plasmid pTA163 lost their abilities to catalyze trans-anethole. Heterologously expressed ORF 10 (1,047 nucleotides [nt]) under a T7 promoter in E. coli catalyzed oxidative cleavage of a propenyl group of trans-anethole to an aldehyde group, resulting in the production of para-anisaldehyde, and this gene was designated tao (trans-anethole oxygenase). The deduced amino acid sequence of TAO had the highest identity (34%) to a hypothetical protein of Agrobacterium vitis S4 and likely contained a flavin-binding site. Preferred incorporation of an oxygen molecule from water into p-anisaldehyde using (18)O-labeling experiments indicated stereo preference of TAO for hydrolysis of the epoxide group. Interestingly, unlike the narrow substrate range of isoeugenol monooxygenase from Pseudomonas putida IE27 and Pseudomonas nitroreducens Jin1, TAO from P. putida JYR-1 catalyzed isoeugenol, O-methyl isoeugenol, and isosafrole, all of which contain the 2-propenyl functional group on the aromatic ring structure. Addition of NAD(P)H to the ultrafiltered cell extracts of E. coli (pTA163) increased the activity of TAO. Due to the relaxed substrate range of TAO, it may be utilized for the production of various fragrance compounds from plant phenylpropanoids in the future.
Topics: Allylbenzene Derivatives; Anisoles; Base Sequence; Benzaldehydes; Biotransformation; Chromatography, High Pressure Liquid; DNA Primers; Escherichia coli; Gene Library; Genes, Bacterial; Mass Spectrometry; Metabolic Networks and Pathways; Molecular Sequence Data; Mutagenesis; Oxidation-Reduction; Oxygen Isotopes; Oxygenases; Plasmids; Pseudomonas putida; Sequence Analysis, DNA
PubMed: 22610435
DOI: 10.1128/AEM.00781-12 -
International Journal of Molecular... 2012In this study, 207 strains of aerobic and facultatively anaerobic cellulolytic bacteria were isolated from the gut of Holotrichia parallela larvae. These bacterial...
In this study, 207 strains of aerobic and facultatively anaerobic cellulolytic bacteria were isolated from the gut of Holotrichia parallela larvae. These bacterial isolates were assigned to 21 genotypes by amplified ribosomal DNA restriction analysis (ARDRA). A partial 16S rDNA sequence analysis and standard biochemical and physiological tests were used for the assignment of the 21 representative isolates. Our results show that the cellulolytic bacterial community is dominated by the Proteobacteria (70.05%), followed by the Actinobacteria (24.15%), the Firmicutes (4.35%), and the Bacteroidetes (1.45%). At the genus level, Gram-negative bacteria including Pseudomonas, Ochrobactrum, Rhizobium, Cellulosimicrobium, and Microbacterium were the predominant groups, but members of Bacillus, Dyadobacter, Siphonobacter, Paracoccus, Kaistia, Devosia, Labrys, Ensifer, Variovorax, Shinella, Citrobacter, and Stenotrophomonas were also found. Furthermore, our results suggest that a significant amount of bacterial diversity exists among the cellulolytic bacteria, and that Siphonobacter aquaeclarae, Cellulosimicrobium funkei, Paracoccus sulfuroxidans, Ochrobactrum cytisi, Ochrobactrum haematophilum, Kaistia adipata, Devosia riboflavina, Labrys neptuniae, Ensifer adhaerens, Shinella zoogloeoides, Citrobacter freundii, and Pseudomonas nitroreducens are reported to be cellulolytic for the first time in this study. Our results indicate that the scarab gut is an attractive source for the study of novel cellulolytic microorganisms and enzymes useful for cellulose degradation.
Topics: Animals; Bacteria; Cellulase; Cellulose; Coleoptera; Gastrointestinal Tract; Larva; Microbial Sensitivity Tests; Molecular Sequence Data
PubMed: 22489111
DOI: 10.3390/ijms13032563