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J. Microbiol. Biotechnol. 2018; 28(2): 330-337

Published online February 28, 2018 https://doi.org/10.4014/jmb.1709.09002

Copyright © The Korean Society for Microbiology and Biotechnology.

Genome Analysis of Naphthalene-Degrading Pseudomonas sp. AS1 Harboring the Megaplasmid pAS1

Jisun Kim 1 and Woojun Park 1*

Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea

Correspondence to:Woojun Park

Received: September 1, 2017; Accepted: November 21, 2017

Abstract

Polycyclic aromatic hydrocarbons (PAHs), including naphthalene, are widely distributed in nature. Naphthalene has been regarded as a model PAH compound for investigating the mechanisms of bacterial PAH biodegradation. Pseudomonas sp. AS1 isolated from an arseniccontaminated site is capable of growing on various aromatic compounds such as naphthalene, salicylate, and catechol, but not on gentisate. The genome of strain AS1 consists of a 6,126,864 bp circular chromosome and the 81,841 bp circular plasmid pAS1. Pseudomonas sp. AS1 has multiple dioxygenases and related enzymes involved in the degradation of aromatic compounds, which might contribute to the metabolic versatility of this isolate. The pAS1 plasmid exhibits extremely high similarity in size and sequences to the well-known naphthalene-degrading plasmid pDTG1 in Pseudomonas putida strain NCIB 9816-4. Two gene clusters involved in the naphthalene degradation pathway were identified on pAS1. The expression of several nah genes on the plasmid was upregulated by more than 2-fold when naphthalene was used as a sole carbon source. Strains have been isolated at different times and places with different characteristics, but similar genes involved in the degradation of aromatic compounds have been identified on their plasmids, which suggests that the transmissibility of the plasmids might play an important role in the adaptation of the microorganisms to mineralize the compounds.

Keywords: Pseudomonas frederiksbergensis, naphthalene degradation, polycyclic aromatic hydrocarbons(PAHs), horizontal gene transfer, plasmid

Body

Polycyclic aromatic hydrocarbons (PAHs) and their derivatives are widespread in the natural environment [1-3] and can contaminate the ecosystem for a long time as a result of their low solubility in water and their absorption to small particles [2, 4]. Various bacterial strains have been discovered that degrade low-molecular-weight PAHs as part of their metabolism [5-8]. One of the simplest PAHs is naphthalene, which has been widely studied and referred to as a model compound for investigating the mechanisms of bacterial biodegradation [3, 5]. Microbial naphthalene metabolism and the genetic regulations involved in the degradation pathway are extensively characterized in several bacterial strains, particularly the Pseudomonas species [9-13].

Pseudomonas sp. AS1 was first isolated from an arsenic-contaminated site in Gwangju, Kyunggi-Do, South Korea [7]. Pseudomonas sp. AS1 is able to grow on naphthalene, salicylate, and catechol, but not on gentisate (Fig. 1) [7]. In our previous study, PCR analysis using degenerate primers showed that partial regions of the genes involved in naphthalene degradation, which include nahA (encoding naphthalene dioxygenase), nahG (encoding salicylate hydroxylase), and nahR (encoding LysR-type regulator) in Pseudomonas sp. AS1, were identical to those of P. putida NCIB 9816-4 [7]. Thus, Pseudomonas sp. AS1 might possess the classical naphthalene degradation pathway in which salicylate can be converted into acetyl coenzyme A and pyruvate. Salicylate is the main secreted metabolic intermediate of Pseudomonas sp. AS1 in the presence of naphthalene as the sole carbon source, which has been shown by NMR spectroscopy and high-performance liquid chromatography [8]. Microbial interaction in naphthalene-amended conditions between Pseudomonas sp. AS1 and Acinetobacter oleivorans DR1, a bacterial strain that cannot degrade naphthalene, was found to be mediated by salicylate, which was able to promote the growth of A. oleivorans DR1 (Fig. 1) [8]. The salicylate generated by Pseudomonas sp. AS1 during commensal metabolic interactions might be passively taken up by A. oleivorans DR1, where it functions as a growth-supporting factor by inducing salicylate hydroxylase [8].

Figure 1. Test of Pseudomonas sp. AS1 growth under various aromatic hydrocarbons. (A) Growth support of naphthalene-degrading Pseudomonas sp. AS1 toward non-naphthalene-degrading A. oleivorans DR1. Cells were inoculated alone or mixed in minimal basal salts (MSB medium containing 0.5% naphthalene as the sole carbon source). Plating on MSB plate with selective substrates (2% glucose for Pseudomonas sp. AS1 and 2% paraffin for A. oleivorans DR1) was conducted to calculate the CFU. (B-L) Growth of Pseudomonas sp. AS1 with various aromatic hydrocarbons. Cells were grown at 30°C in MSB medium supplemented with various compounds and OD600 values were measured at the indicated time points.

To obtain the detailed genetic information involved in naphthalene degradation, we sequenced the whole genome of Pseudomonas sp. AS1. Genomic DNA was extracted using the Wizard Genomic DNA purification Kit (Promega, USA). Whole-genome sequencing was performed by the Pacific Biosciences RSII Single Molecule Real Time (SMRT) sequencing technology (Pacific Biosciences, USA) with a SMRTbell template library. A total of 184,024 reads with a mean read length of 8,088 bp were generated. The complete genome was assembled using the Hierarchical Genome Assembly Process ver. 3.0, and gene annotation was achieved by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline.

The genomic features of Pseudomonas sp. AS1 are summarized in Table 1, and consist of a single circular chromosome with a circular plasmid (Fig. 2). The sizes of the chromosome and plasmid were 6,126,864 bp with a GC content of 58.9%, and 81,841 bp with a GC content of 56.2%, respectively. The Pseudomonas sp. AS1 chromosome contains 5,634 coding sequences (CDS), 66 tRNA genes, 22 rRNA genes, and 158 pseudogenes. There are 99 CDS in the plasmid region. The predicted genes were functionally characterized using Pfam [14], Cluster of Orthologous Groups (COG) [15, 16], and KEGG [17] databases; 82.47%, 70.08%, and 28.28% of the CDS were functionally assigned on the basis of Pfam, COG, and KEGG, respectively. A total of 5,735 CDS were classified using the COG database [15, 16]. The COG functional classification is shown in Fig. S1. The most abundant group is involved in amino acid metabolism and transport (COG category E, 7.4%), followed by a group involved in transcription (COG category K, 6.9%). This pattern of COG classification was commonly found in soil or water-derived pollutant-degrading Pseudomonas strains having genomes approximately 6.1-6.3 Mbp in size (Fig. S2). The clustered regularly interspaced short palindromic repeat (CRISPR) gene sequences were found using Integrated Microbial Genomes (IMG; https://img.jgi.doe.gov/). CRISPRs are elaborate defense strategies against bacteriophage predation [18]. The genome of Pseudomonas sp. AS1 contained only one possible CRISPR consisting of 188 bp in size that possessed two spacers without predicted cas gene (Tables 1 and S1). The 45 genomic islands were identified in the genome sequence of Pseudomonas sp. AS1 using the online integrated GI prediction tool (IslandViewer 4; http://www.pathogenomics. sfu.ca/islandviewer/). The GC contents of predicted GIs (44.4% to 62.6%) were quite different from that of the whole chromosome and plasmid of Pseudomonas sp. AS1 (58.9%and 56.2%, respectively) (Table S2). Predicted GIs were involved in transport, replication, and hydrocarbon degradation (Table S2). Many of the GIs carrying genes encoding mobile elements, such as integrases and transposases, provide evidence regarding the genomic plasticity of Pseudomonas sp. AS1 as a result of horizontal gene transfers and genetic rearrangements in the genome of Pseudomonas sp. AS1. The IMG database predicted 18 genes to be putative horizontally transferred genes in the genome sequence of Pseudomonas sp. AS1 (Table S3). Most of the genes listed in Table S3 were possibly transferred from other proteobacteria. Pseudomonas sp. AS1 might acquire several genes from different donors and finally have the current set of genome contents appropriate for its habitat. Thus, the presence of CRISPR, the large number of genomic islands, and putative horizontally transferred genes in the genome of Pseudomonas sp. AS1 suggest that complex genetic rearrangements may have occurred as a consequence of adaptive evolution of this strain.

Table 1 . General features of the Pseudomonas sp. AS1 genome..

Genetic elementChromosomePlasmid (pAS1)
Size (bp)6,126,86481,841
GC content (%)58.9 %56.2 %
Total coding DNA sequence (CDS)563499
rRNA genes (5S, 16S, 23S)8, 7, 70
tRNA genes660
No. of CRISPR10
No. of genomic islands405
GenBank accession numberCP018319CP018320

Figure 2. Circular map of the chromosome and the plasmid of Pseudomonas sp. AS1. From the outside to the center: genes on the forward strand (colored by COG categories), genes on the reverse strand (colored by COG categories), RNA genes (tRNAs, green; rRNAs, red), GC content, and GC skew.

The plasmid in Pseudomonas sp. AS1 (hereafter referred to as pAS1) contains the IncP-9 plasmid backbone, which has a region involved in plasmid transfer (tra, position 51908-57689), conjugation (mpf, position 60,813-71,545), plasmid partitioning (par, position 70,247-73,535), and plasmid replication including oriV (rep, position 73,536-75,269) (Fig. 3). Interestingly, pAS1 exhibits striking similarities in size and sequence to the pDTG1 plasmid that carries naphthalene catabolic genes (nah) from Pseudomonas putida strain NCIB 9816-4 [9]. Five mismatch nucleotides in the nah upper pathway were identified as well as 1,201 bp in differences between pDTG1 and pAS1. Five missing nucleotides corresponding to positions 26,623, 55,994, 58,070, 60,906, and 62,294 of pDTG1 were identified in pAS1. The most distinct difference between the two plasmids was a 1,196 bp region absent in pAS1 corresponding to position 49,370-50,565 of pDTG1, which has an insertion sequence element (transposase) between nahT and nahG (encoding salicylate hydroxylase) consisting of the naphthalene catabolic pathway genes [9]. A set of genes involved in the degradation of naphthalene may have been inserted into each backbone of pDTG1 and pAS1 at different sites because plasmids have been found individually, indicating multiple independent acquisitions of the degradation trait and global distribution of the IncP-9 plasmid backbone in the environment.

Figure 3. (A) Alignment of the linear maps of the plasmids pDTG1 and pAS1 with a focus on the naphthalene degradation pathway and (B) expression analysis of nah genes in Pseudomonas sp. AS1 under naphthalene degradation.

Naphthalene degradation is organized into upper and lower pathways [3]. The upper pathway enzymes are involved in the conversion of naphthalene to salicylate. This pathway comprises 10 genes organized in the order nahAaAbAcAdBFCQED. The lower pathway enzymes are encoded by nahGTHINLOMKJY and are involved in the oxidation of salicylate to pyruvate and acetyl coenzyme A [3]. According to our genome sequencing and analysis, pAS1 has all 21 genes consisting of the upper and lower pathways as well as the nahR-encoding transcriptional regulator required for the induction of the nah genes (Fig. 3). To determine the expression of genes involved in naphthalene degradation, we compared the mRNA expression levels of Pseudomonas sp. AS1 via quantitative reverse transcription-PCR (qRT-PCR) under two growth conditions: in the presence of naphthalene as a sole carbon source and under glucose-growing conditions. The qRT-PCR was conducted as described previously [19]. The cells were incubated until the exponential phase (OD600 ~ 0.3), at which point the cells were collected for RNA isolation. Relative gene expression was calculated on the basis of cells grown in minimal salts basal (MSB) medium supplemented with 10 mM glucose. All of the tested nah genes showed more than a 2-fold expression change when Pseudomonas sp. AS1 was grown in the presence of naphthalene (Fig. 3B). Naphthalene cannot be degraded through the gentisate pathway in Pseudomonas sp. AS1 because this strain cannot utilize gentisate as a carbon source (Fig. 1) owing to the absence of gentisate 1,2-dioxygenase as well as a lack of expression for hmgA encoding homogentisate 1,2-dioxygenase during naphthalene degradation (Fig. 3B). Therefore, Pseudomonas sp. AS1 might have a naphthalene degradation pathway via salicylate as a central intermediate, which can be converted into acetyl coenzyme A and pyruvate.

The 16S rRNA sequence of Pseudomonas sp. AS1 has over 99% DNA identities with those of Pseudomonas frederiksbergensis strains. The average nucleotide identity analysis of strain AS1 with P. frederiksbergensis strains revealed a similarity index with P. frederiksbergensis ERDD5:01 (84.6%), P. frederiksbergensis BS3655 (97.3%), and P. frederiksbergensis SI8 (82.2%), suggesting Pseudomonas sp. AS1 is closely related to P. frederiksbergensis BS3655. P. frederiksbergensis strains are commonly capable of degrading aromatic compounds [7, 20, 21]. Pseudomonas sp. AS1 can grow in MSB medium supplemented with various aromatic compounds, including the aforementioned naphthalene as a sole carbon source, as well as catechol, benzene, sodium salicylate, salicylic acid, salicylaldehyde, benzoic acid, 3-hydroxylbenzoic acid, 4-hydroxylbenzoic acid, and 3,4-dihydroxylbenzoate (Fig. 1). There was no growth in the presence of hexadecane and dodecane, which might be due to the absence of alkane monooxygenase required for alkane degradation. Further studies on alkane degradation by Pseudomonas sp. AS1 are necessary because alkane degradation generally depends on the chain length of alkanes and involvement of cytochrome P450s and hydroxylases with unknown function. Pseudomonas sp. AS1 has an abundance of genes encoding hydroxylases and related genes, including monooxygenase and dioxygenase, genes that might enable the high utilization of various aromatic compounds (Table 2). The Pseudomonas sp. AS1 genome revealed 34 dioxygenases, including benzoate dioxygenase (PFAS1_RS22900, PFAS1_RS22905, and PFAS1_RS22910), protocatechuate 3,4-dioxygenase (PFAS1_RS18060 and PFAS1_RS18065), and catechol 1,2-dioxgenase (PFAS1_RS22890). Three homologs of genes coding for taurine dioxygenases (PFAS1_RS09965, PFAS1_RS10310, and PFAS1_RS23020) and eight predicted monooxygenase genes are also present (Table 2). In addition, the genome encodes 87 putative hydrolases, more than 375 transferases, and 234 dehydrogenases, all of which have uncharacterized functions and belong to a number of different protein families. Related to the bioremediation process, the detected ssuFBCDAE operon (from PFAS1_RS12590 to PFAS1_RS12615) might allow for sustainable growth on aromatic and aliphatic sulfonates, and 14 glutathione S-transferases may be involved in detoxification processes. In addition, PAHs or toxic metabolic intermediates can generate reactive oxygen species (ROS) under the biodegradation processes [2, 7, 10]. The genome of Pseudomonas sp. AS1 contains two oxidative stress response regulators, SoxR and OxyR (encoded by PFAS1_RS02805 and PFAS1_RS11840, respectively) to protect against and relieve ROS-derived oxidative stress through the regulation of the genes. P. frederiksbergensis strains have been isolated from various environmental conditions, and all genome-sequenced strains showed differences in genome size, GC content, and plasmids (Table 3). Bacterial cells can obtain exogenous genes via horizontal gene transfer, which is indispensable for survival and adaptation to harsh environmental conditions [22-24]. We expect that Pseudomonas sp. AS1 acquired its plasmid for this reason during adaptation to contaminated soil. To explore the genetic evolution among P. frederiksbergensis strains, it will be necessary to perform comparative genomics. In that respect, the complete genome sequence of Pseudomonas sp. AS1 will provide clues for the early stages of genetic research on P. frederiksbergensis species.

Table 2 . Genes encoding hydroxylases and related genes in Pseudomonas sp. AS1..

Locus TagGene Product Name
PFAS1_RS01505acireductone dioxygenase apoprotein
PFAS1_RS02800antibiotic biosynthesis monooxygenase
PFAS1_RS031204,5-DOPA dioxygenase extradiol
PFAS1_RS04745intradiol ring-cleavage dioxygenase
PFAS1_RS04850heme oxygenase
PFAS1_RS05325p-hydroxybenzoate 3-monooxygenase
PFAS1_RS06565 (hmgA)homogentisate 1,2-dioxygenase
PFAS1_RS07555glyoxalase/bleomycin resistance protein/dioxygenase superfamily protein
PFAS1_RS09965taurine dioxygenase
PFAS1_RS10310taurine dioxygenase
PFAS1_RS10360p-aminobenzoate N-oxygenase AurF
PFAS1_RS10865DOPA 4,5-dioxygenase
PFAS1_RS12600 (ssuD)alkanesulfonate monooxygenase
PFAS1_RS12890p-aminobenzoate N-oxygenase AurF
PFAS1_RS13525gamma-butyrobetaine dioxygenase
PFAS1_RS13895lysine 2-monooxygenase
PFAS1_RS14470p-aminobenzoate N-oxygenase AurF
PFAS1_RS152204-hydroxyphenylpyruvate dioxygenase
PFAS1_RS16755nitric oxide dioxygenase
PFAS1_RS18060 (pcaH)protocatechuate 3,4-dioxygenase, beta subunit
PFAS1_RS18065protocatechuate 3,4-dioxygenase, alpha subunit
PFAS1_RS22890catechol 1,2-dioxygenase
PFAS1_RS22900benzoate 1,2-dioxygenase, alpha subunit
PFAS1_RS22905benzoate/toluate 1,2-dioxygenase beta subunit
PFAS1_RS22910benzoate/toluate 1,2-dioxygenase reductase subunit
PFAS1_RS229151,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase
PFAS1_RS23020taurine dioxygenase
PFAS1_RS23040ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase
PFAS1_RS24315tryptophan 2-monooxygenase precursor
PFAS1_RS24325phenylpropionate dioxygenase, large terminal subunit
PFAS1_RS24455flavin-dependent oxidoreductase
PFAS1_RS25260nitronate monooxygenase
PFAS1_RS25375 (hppD)4-hydroxyphenylpyruvate dioxygenase
PFAS1_RS25815 (sfnG)dimethylsulfone monooxygenase
PFAS1_RS26480FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family
PFAS1_RS28660 (nahAc)*ferredoxin-NAD(P)+ reductase (naphthalene dioxygenase ferredoxin-specific)
PFAS1_RS28665 (nahAb) *naphthalene 1,2-dioxygenase system ferredoxin subunit
PFAS1_RS28670 (nahAc) *naphthalene 1,2-dioxygenase subunit alpha
PFAS1_RS28675 (nahAd) *naphthalene 1,2-dioxygenase subunit beta
PFAS1_RS28680 (nahB) *cis-1,2-dihydro-1,2-dihydroxynaphthalene/dibenzothiophene dihydrodiol dehydrogenase
PFAS1_RS28685 (nahF) *salicylaldehyde dehydrogenase
PFAS1_RS28690 (nahC) *1,2-dihydroxynaphthalene dioxygenase
PFAS1_RS28700 (nahE) *trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
PFAS1_RS28705 (nahD) *2-hydroxychromene-2-carboxylate isomerase
PFAS1_RS28730 *N-ethylmaleimide reductase
PFAS1_RS28815 (nahJ) *4-oxalocrotonate tautomerase
PFAS1_RS28820 (nahK) *4-oxalocrotonate decarboxylase
PFAS1_RS28825 (nahM) *4-hydroxy-2-oxovalerate aldolase
PFAS1_RS28830 (nahO) *acetaldehyde dehydrogenase
PFAS1_RS28835 (nahL) *2-oxopent-4-enoate/cis-2-oxohex-4-enoate hydratase
PFAS1_RS28840 (nahN) *2-hydroxymuconate semialdehyde hydrolase
PFAS1_RS28845 (nahI) *2-hydroxymuconate semialdehyde dehydrogenase
PFAS1_RS28850 (nahH) *catechol 2,3-dioxygenase
PFAS1_RS28865 (nahG) *salicylate hydroxylase

*Located on the plasmid of Pseudomonas sp. AS1..


Table 3 . Comparative features of all sequenced Pseudomonas frederiksbergensis genomes..

StrainIsolation siteBiodegradationaSize (Mb)GC (%)Plasmid (bp)Assembly levelReference/ source
AS1Arsenic-contaminated soil, KoreaNaphthalene, various aromatic hydrocarbon compounds6.2258.861 (81,841 bp)CompleteThis study; [7, 8]
ERDD5:01Glacial stream, IndiaNDb6.1258.481 (371,069 bp)CompleteNCBI BioProjects: PRJNA350793
BS3655NDND6.3958.90NDContigNCBI BioProjects: PRJEB16448
SI8Desert soil, KuwaitToluene, ethylbenzene, and propylbenzene6.5760.50NDContig[21]
JAJ28Coal gasification site, DenmarkPhenanthrene-degradingNDNDNDND[20]

aExperimentally determined..

bNot determined..


Nucleotide Sequence Accession Number

The complete genome sequence of Pseudomonas sp. AS1 has been deposited in NCBI under the GenBank accession numbers CP018319 (chromosome) and CP018320 (plasmid).

Supplemental Materials

Acknowledgments

This research was supported by the Basic Science Research Program through the National Research Foundation (NRF) of Korea funded by the Ministry of Education, Science and Technology (No. NRF-2015R1C1A2A01054058). This work was also supported by a grant (NRF-2017R1A2B4005838 to W.P.) of the NRF of Korea.

Fig 1.

Figure 1.Test of Pseudomonas sp. AS1 growth under various aromatic hydrocarbons. (A) Growth support of naphthalene-degrading Pseudomonas sp. AS1 toward non-naphthalene-degrading A. oleivorans DR1. Cells were inoculated alone or mixed in minimal basal salts (MSB medium containing 0.5% naphthalene as the sole carbon source). Plating on MSB plate with selective substrates (2% glucose for Pseudomonas sp. AS1 and 2% paraffin for A. oleivorans DR1) was conducted to calculate the CFU. (B-L) Growth of Pseudomonas sp. AS1 with various aromatic hydrocarbons. Cells were grown at 30°C in MSB medium supplemented with various compounds and OD600 values were measured at the indicated time points.
Journal of Microbiology and Biotechnology 2018; 28: 330-337https://doi.org/10.4014/jmb.1709.09002

Fig 2.

Figure 2.Circular map of the chromosome and the plasmid of Pseudomonas sp. AS1. From the outside to the center: genes on the forward strand (colored by COG categories), genes on the reverse strand (colored by COG categories), RNA genes (tRNAs, green; rRNAs, red), GC content, and GC skew.
Journal of Microbiology and Biotechnology 2018; 28: 330-337https://doi.org/10.4014/jmb.1709.09002

Fig 3.

Figure 3.(A) Alignment of the linear maps of the plasmids pDTG1 and pAS1 with a focus on the naphthalene degradation pathway and (B) expression analysis of nah genes in Pseudomonas sp. AS1 under naphthalene degradation.
Journal of Microbiology and Biotechnology 2018; 28: 330-337https://doi.org/10.4014/jmb.1709.09002

Table 1 . General features of the Pseudomonas sp. AS1 genome..

Genetic elementChromosomePlasmid (pAS1)
Size (bp)6,126,86481,841
GC content (%)58.9 %56.2 %
Total coding DNA sequence (CDS)563499
rRNA genes (5S, 16S, 23S)8, 7, 70
tRNA genes660
No. of CRISPR10
No. of genomic islands405
GenBank accession numberCP018319CP018320

Table 2 . Genes encoding hydroxylases and related genes in Pseudomonas sp. AS1..

Locus TagGene Product Name
PFAS1_RS01505acireductone dioxygenase apoprotein
PFAS1_RS02800antibiotic biosynthesis monooxygenase
PFAS1_RS031204,5-DOPA dioxygenase extradiol
PFAS1_RS04745intradiol ring-cleavage dioxygenase
PFAS1_RS04850heme oxygenase
PFAS1_RS05325p-hydroxybenzoate 3-monooxygenase
PFAS1_RS06565 (hmgA)homogentisate 1,2-dioxygenase
PFAS1_RS07555glyoxalase/bleomycin resistance protein/dioxygenase superfamily protein
PFAS1_RS09965taurine dioxygenase
PFAS1_RS10310taurine dioxygenase
PFAS1_RS10360p-aminobenzoate N-oxygenase AurF
PFAS1_RS10865DOPA 4,5-dioxygenase
PFAS1_RS12600 (ssuD)alkanesulfonate monooxygenase
PFAS1_RS12890p-aminobenzoate N-oxygenase AurF
PFAS1_RS13525gamma-butyrobetaine dioxygenase
PFAS1_RS13895lysine 2-monooxygenase
PFAS1_RS14470p-aminobenzoate N-oxygenase AurF
PFAS1_RS152204-hydroxyphenylpyruvate dioxygenase
PFAS1_RS16755nitric oxide dioxygenase
PFAS1_RS18060 (pcaH)protocatechuate 3,4-dioxygenase, beta subunit
PFAS1_RS18065protocatechuate 3,4-dioxygenase, alpha subunit
PFAS1_RS22890catechol 1,2-dioxygenase
PFAS1_RS22900benzoate 1,2-dioxygenase, alpha subunit
PFAS1_RS22905benzoate/toluate 1,2-dioxygenase beta subunit
PFAS1_RS22910benzoate/toluate 1,2-dioxygenase reductase subunit
PFAS1_RS229151,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase
PFAS1_RS23020taurine dioxygenase
PFAS1_RS23040ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase
PFAS1_RS24315tryptophan 2-monooxygenase precursor
PFAS1_RS24325phenylpropionate dioxygenase, large terminal subunit
PFAS1_RS24455flavin-dependent oxidoreductase
PFAS1_RS25260nitronate monooxygenase
PFAS1_RS25375 (hppD)4-hydroxyphenylpyruvate dioxygenase
PFAS1_RS25815 (sfnG)dimethylsulfone monooxygenase
PFAS1_RS26480FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family
PFAS1_RS28660 (nahAc)*ferredoxin-NAD(P)+ reductase (naphthalene dioxygenase ferredoxin-specific)
PFAS1_RS28665 (nahAb) *naphthalene 1,2-dioxygenase system ferredoxin subunit
PFAS1_RS28670 (nahAc) *naphthalene 1,2-dioxygenase subunit alpha
PFAS1_RS28675 (nahAd) *naphthalene 1,2-dioxygenase subunit beta
PFAS1_RS28680 (nahB) *cis-1,2-dihydro-1,2-dihydroxynaphthalene/dibenzothiophene dihydrodiol dehydrogenase
PFAS1_RS28685 (nahF) *salicylaldehyde dehydrogenase
PFAS1_RS28690 (nahC) *1,2-dihydroxynaphthalene dioxygenase
PFAS1_RS28700 (nahE) *trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
PFAS1_RS28705 (nahD) *2-hydroxychromene-2-carboxylate isomerase
PFAS1_RS28730 *N-ethylmaleimide reductase
PFAS1_RS28815 (nahJ) *4-oxalocrotonate tautomerase
PFAS1_RS28820 (nahK) *4-oxalocrotonate decarboxylase
PFAS1_RS28825 (nahM) *4-hydroxy-2-oxovalerate aldolase
PFAS1_RS28830 (nahO) *acetaldehyde dehydrogenase
PFAS1_RS28835 (nahL) *2-oxopent-4-enoate/cis-2-oxohex-4-enoate hydratase
PFAS1_RS28840 (nahN) *2-hydroxymuconate semialdehyde hydrolase
PFAS1_RS28845 (nahI) *2-hydroxymuconate semialdehyde dehydrogenase
PFAS1_RS28850 (nahH) *catechol 2,3-dioxygenase
PFAS1_RS28865 (nahG) *salicylate hydroxylase

*Located on the plasmid of Pseudomonas sp. AS1..


Table 3 . Comparative features of all sequenced Pseudomonas frederiksbergensis genomes..

StrainIsolation siteBiodegradationaSize (Mb)GC (%)Plasmid (bp)Assembly levelReference/ source
AS1Arsenic-contaminated soil, KoreaNaphthalene, various aromatic hydrocarbon compounds6.2258.861 (81,841 bp)CompleteThis study; [7, 8]
ERDD5:01Glacial stream, IndiaNDb6.1258.481 (371,069 bp)CompleteNCBI BioProjects: PRJNA350793
BS3655NDND6.3958.90NDContigNCBI BioProjects: PRJEB16448
SI8Desert soil, KuwaitToluene, ethylbenzene, and propylbenzene6.5760.50NDContig[21]
JAJ28Coal gasification site, DenmarkPhenanthrene-degradingNDNDNDND[20]

aExperimentally determined..

bNot determined..


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