Genomic characterization of an uncommon Delftia acidovorans isolate obtained from a Bulgarian immunocompetent outpatient diagnosed with bronchitis.

Delftia acidovorans is an aerobic, non-fermenting Gram-negative bacterium (NFGNB), found in soil, water and hospital environments. It is rarely clinically significant, most commonly affecting hospitalized or immunocompromised patients. The present study aimed to explore the genomic characteristics of a Bulgarian clinical D. acidovorans isolate (designated Dac759) in comparison to all strains of this species with available genomes in the NCBI Genome database (n = 34). Dac759 was obtained in 2021 from the sputum of a 65-year-old female immunocompetent outpatient with bronchitis. Species identification using MALDI-TOF mass spectrometry, antimicrobial susceptibility testing, whole-genome sequencing (WGS), and phylogenomic analysis were performed. The isolate demonstrated high-level resistance to colistin (16 mg L-1); resistance to gentamicin; reduced susceptibility to piperacillin, piperacillin-tazobactam, ceftazidime, cefepime, ciprofloxacin, and levofloxacin; and susceptibility to imipenem, meropenem, amikacin, and tobramycin. The observed genome size (6.43 Mb) and GC content (66.76%) were comparable with the accessible data from sequenced D. acidovorans genomes. A limited number of resistance determinants were identified in the assembled genome as follows: blaOXA-459, emrE, oqxB, and mexCD-oprJ. The phylogenomic analysis indicated a high heterogenicity of the included D. acidovorans genomes. In conclusion, to the best of our knowledge, this is the first documented case of a clinically relevant D. acidovorans isolate in Bulgaria. Unlike the majority of reports in the literature, Dac759 affected a patient with no malignancies or other preexisting comorbidities. With this in mind, its genome sequence is a valuable resource for the fundamental study of uncommon bacterial pathogens of public health importance.

Whole-Genome Sequencing of a Multidrug-Resistant Strain: Delftia acidovorans B408.

BACKGROUND: Delftia acidovorans is distributed widely in the environment and has the potential to promote the growth of plants and degrade organic pollutants. However, it is also an opportunistic pathogen for human and many reports demonstrated that D. acidovorans has strong resistance to aminoglycosides and polymyxins. OBJECTIVE: The aim of this work was to reveal the antibiotic resistance genes and pathogenic genes in a novel conditional pathogenic strain-D. acidovorans B804, which was isolated from the radiation-polluted soil from Xinjiang Uyghur Autonomous Region, China. METHODS: The antibiotic resistance test was performed according to the Kirby-Bauer disk diffusion method and evaluated by the standards of the Clinical and Laboratory Standards Institute guidelines. The genome of D. acidovorans B804 was sequenced by a PacBio RS II and Illumina HiSeq 4000 platform in Shanghai Majorbio Biopharm Technology Co., Ltd. (Shanghai, China). RESULTS: The multidrug resistance phenotypes of D. acidovorans B804 was experimentally confirmed and its genome was sequenced. The total size of D. acidovorans B804 genome was 6,661,314 bp with a GC content of 66.73%. 403 genes associated with antibiotic resistances were predicted. Meanwhile, 89 pathogenic genes were also predicted and 17 of these genes might be capable of causing diseases to human, such as infections and salmonellosis. CONCLUSIONS: This genomic information can be used as a reference sequence for comparative genomic studies. The results provided more insights regarding the pathogenesis and drug resistance mechanism of D. acidovorans, which will be meaningful for developing more effective therapies toward D. acidovorans-related diseases.

Delftia acidovorans secretes substances that inhibit the growth of Staphylococcus epidermidis through TCA cycle-triggered ROS production.

The proportion of Staphylococcus aureus in the skin microbiome is associated with the severity of inflammation in the skin disease atopic dermatitis. Staphylococcus epidermidis, a commensal skin bacterium, inhibits the growth of S. aureus in the skin. Therefore, the balance between S. epidermidis and S. aureus in the skin microbiome is important for maintaining healthy skin. In the present study, we demonstrated that the heat-treated culture supernatant of Delftia acidovorans, a member of the skin microbiome, inhibits the growth of S. epidermidis, but not that of S. aureus. Comprehensive gene expression analysis by RNA sequencing revealed that culture supernatant of D. acidovorans increased the expression of genes related to glycolysis and the tricarboxylic acid cycle (TCA) cycle in S. epidermidis. Malonate, an inhibitor of succinate dehydrogenase in the TCA cycle, suppressed the inhibitory effect of the heat-treated culture supernatant of D. acidovorans on the growth of S. epidermidis. Reactive oxygen species production in S. epidermidis was induced by the heat-treated culture supernatant of D. acidovorans and suppressed by malonate. Further, the inhibitory effect of the heat-treated culture supernatant of D. acidovorans on the growth of S. epidermidis was suppressed by N-acetyl-L-cysteine, a free radical scavenger. These findings suggest that heat-resistant substances secreted by D. acidovorans inhibit the growth of S. epidermidis by inducing the production of reactive oxygen species via the TCA cycle.

Transcriptomics reveal core activities of the plant growth-promoting bacterium Delftia acidovorans RAY209 during interaction with canola and soybean roots.

The plant growth-promoting rhizobacterium Delftia acidovorans RAY209 is capable of establishing strong root attachment during early plant development at 7 days post-inoculation. The transcriptional response of RAY209 was measured using RNA-seq during early (day 2) and sustained (day 7) root colonization of canola plants, capturing RAY209 differentiation from a medium-suspended cell state to a strongly root-attached cell state. Transcriptomic data was collected in an identical manner during RAY209 interaction with soybean roots to explore the putative root colonization response to this globally relevant crop. Analysis indicated there is an increased number of significantly differentially expressed genes between medium-suspended and root-attached cells during early soybean root colonization relative to sustained colonization, while the opposite temporal pattern was observed for canola root colonization. Regardless of the plant host, root-attached RAY209 cells exhibited the least amount of differential gene expression between early and sustained root colonization. Root-attached cells of either canola or soybean roots expressed high levels of a fasciclin gene homolog encoding an adhesion protein, as well as genes encoding hydrolases, multiple biosynthetic processes, and membrane transport. Notably, while RAY209 ABC transporter genes of similar function were transcribed during attachment to either canola or soybean roots, several transporter genes were uniquely differentially expressed during colonization of the respective plant hosts. In turn, both canola and soybean plants expressed genes encoding pectin lyase and hydrolases - enzymes with purported function in remodelling extracellular matrices in response to RAY209 colonization. RAY209 exhibited both a core regulatory response and a planthost-specific regulatory response to root colonization, indicating that RAY209 specifically adjusts its cellular activities to adapt to the canola and soybean root environments. This transcriptomic data defines the basic RAY209 response as both a canola and soybean commercial crop and seed inoculant.

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis.

In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples. D. acidovorans was also identified in 16 previously published metagenomes from multiple environments, but detailed-scale single nucleotide polymorphism analysis grouped these into five distinct clades. All of the strains indicated as contaminants fell into one clade. Fragment length anomalies were identified in paired reads mapping to the contaminant clade genotypes only. This finding was used to establish that the DNA was present in specific size selection reagents used during sequencing. Ultimately, the source of the contaminant was identified as bacterial biofilms growing in tubing. On the basis of direct measurement of the rate of fixation of mutations across the period of time in which contamination was occurring, we estimated the time of separation of the contaminant strain from the genomically sequenced ancestral population within a factor of 2. This research serves as a case study of high-resolution microbial forensics and strain tracking accomplished through metagenomics-based comparative genomics. The specific case reported here is unusual in that the study was conducted in the background of a soil metagenome and the conclusions were confirmed by independent methods.IMPORTANCE It is often important to determine the source of a microbial strain. Examples include tracking a bacterium linked to a disease epidemic, contaminating the food supply, or used in bioterrorism. Strain identification and tracking are generally approached by using cultivation-based or relatively nonspecific gene fingerprinting methods. Genomic methods have the ability to distinguish strains, but this approach typically has been restricted to isolates or relatively low-complexity communities. We demonstrate that strain-resolved metagenomics can be applied to extremely complex soil samples. We genotypically defined a soil-associated bacterium and identified it as a contaminant. By linking together snapshots of the bacterial genome over time, it was possible to estimate how long the contaminant had been diverging from a likely source population. The results are congruent with the derivation of the bacterium from a strain isolated in Germany and sequenced a decade ago and highlight the utility of metagenomics in strain tracking.

Microbiological characterization of Delftia acidovorans clinical isolates from patients in an intensive care unit in Brazil.

Delftia acidovorans is an opportunistic agent in several types of infections, both in immunocompromised and immune-competent individuals; its resistance to aminoglycosides and polymyxin, choice drugs for empirical treatment of Gram-negative infections, is remarkable. We report the antimicrobial susceptibility and the genetic relatedness of 24 D. acidovorans strains recovered from tracheal aspirates of 21 adult inpatients hospitalized in an intensive care unit at a Brazilian hospital, from 2012 to 2013. All of the isolates were recovered as pure cultures and in counts above 1,000,000 CFU/mL. None of them were susceptible to polymyxin B, amikacin, gentamicin, or tobramycin; quinolones and trimethoprim-sulfamethoxazole presented varied activities against the isolates, while ß-lactam resistance was not detected. Four clusters were verified in pulsed-field gel electrophoresis analysis, and a major pulsotype comprised 10 strains. A possible, but undetermined common source, can be responsible for this strain dissemination, underscoring the need of reinforcing the adherence to disinfection and infection control standard techniques.

Engineering Delftia acidovorans DSM39 to produce polyhydroxyalkanoates from slaughterhouse waste.

The inexpensive agricultural fatty by-products could be usefully converted to polyhydroxyalkanoates (PHAs) by properly selected and/or developed microbes. Delftia acidovorans DSM39 is a well-known producer of PHAs with high molar fractions of 4-hydroxybutyrate (4HB), but unable to grow on fatty substrates. The aim of this study was to construct a recombinant strain of D. acidovorans DSM39 using fats-containing waste such as udder, lard and tallow, to produce PHAs. The lipC and lipH genes of Pseudomonas stutzeri BT3, proficient lipolytic isolate, were successfully co-expressed into D. acidovorans DSM39 and the resulting recombinant strain displayed high extracellular enzymatic activity on corn oil. The PHAs production from corn oil achieved high levels (26% of cell dry weight, with about 7% of 4HB). Surprisingly, the recombinant strain produced greater values directly from slaughterhouse residues such as udder and lard (43 and 39%, respectively, with almost 7% of 4HB). Moreover, this work proved the ability of the recombinant D. acidovorans strain to produce PHAs with significant percentage of 4HB, without the supplementation of any precursor in the liquid broth. This research paves the way to the efficient one-step conversion of fatty residues into PHAs having valuable properties exploitable in several medical and industrial applications.

Gold biomineralization by a metallophore from a gold-associated microbe.

Microorganisms produce and secrete secondary metabolites to assist in their survival. We report that the gold resident bacterium Delftia acidovorans produces a secondary metabolite that protects from soluble gold through the generation of solid gold forms. This finding is the first demonstration that a secreted metabolite can protect against toxic gold and cause gold biomineralization.

Co-infection with Pseudomonas anguilliseptica and Delftia acidovorans in the European eel, Anguilla anguilla (L.): a case history of an illegally trafficked protected species.

Inspections by customs agents at Barcelona airport discovered 420 kg of contraband glass eels prepared for shipment to Hong Kong. After confiscation of these animals by police, they were transported to holding facilities to be maintained until after a judicial hearing. Upon arrival, they were separated into two groups and held under ambient flow-through conditions in fresh water. During their captivity period, several peaks in mortality occurred and multiple bacterial strains were isolated from moribund animals. Sequencing of 16S rDNA was used to determine specific identity of the isolates. An initial isolation of Pseudomonas anguilliseptica was treated with oxytetracycline. A subsequent isolation of Delftia acidovorans proved resistant to oxytetracycline and was treated with gentamicin in combination with sulphadiazine-trimethoprim. Once the health condition of the animals was stabilized, they were partitioned into groups and subsequently released as part of a restocking effort for the species following the guidelines of Regulation (EC) 1100/2007 (Anon 2007). This represents the first record for both bacterial species in the host Anguilla anguilla in the Spanish Mediterranean.

Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases.

Expression of foreign pathways often results in suboptimal performance due to unintended factors such as introduction of toxic metabolites, cofactor imbalances or poor expression of pathway components. In this study we report a 120% improvement in the production of the isoprenoid-derived sesquiterpene, amorphadiene, produced by an engineered strain of Escherichia coli developed to express the native seven-gene mevalonate pathway from Saccharomyces cerevisiae (Martin et al. 2003). This substantial improvement was made by varying only a single component of the pathway (HMG-CoA reductase) and subsequent host optimization to improve cofactor availability. We characterized and tested five variant HMG-CoA reductases obtained from publicly available genome databases with differing kinetic properties and cofactor requirements. The results of our in vitro and in vivo analyses of these enzymes implicate substrate inhibition of mevalonate kinase as an important factor in optimization of the engineered mevalonate pathway. Consequently, the NADH-dependent HMG-CoA reductase from Delftia acidovorans, which appeared to have the optimal kinetic parameters to balance HMG-CoA levels below the cellular toxicity threshold of E. coli and those of mevalonate below inhibitory concentrations for mevalonate kinase, was identified as the best producer for amorphadiene (54% improvement over the native pathway enzyme, resulting in 2.5mM or 520 mg/L of amorphadiene after 48 h). We further enhanced performance of the strain bearing the D. acidovorans HMG-CoA reductase by increasing the intracellular levels of its preferred cofactor (NADH) using a NAD(+)-dependent formate dehydrogenase from Candida boidinii, along with formate supplementation. This resulted in an overall improvement of the system by 120% resulting in 3.5mM or 700 mg/L amorphadiene after 48 h of fermentation. This comprehensive study incorporated analysis of several key parameters for metabolic design such as in vitro and in vivo kinetic performance of variant enzymes, intracellular levels of protein expression, in-pathway substrate inhibition and cofactor management to enable the observed improvements. These metrics may be applied to a broad range of heterologous pathways for improving the production of biologically derived compounds.

(R,S)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.

We investigated the effect of (R,S)-dichlorprop herbicide addition to soil microcosms on the degrading indigenous microbial community by targeting multiple α-ketoglutarate-dependent (α-KG) dioxygenase-encoding genes (rdpA, sdpA and tfdA group I) at both gene and transcript level. The soil microbial community responded with high growth of potential degraders as measured by the abundance of dioxygenase-encoding genes using quantitative real-time PCR (qPCR). rdpA DNA was not detectable in unamended soil but reached over 106 copies g⁻¹ soil after amendment. sdpA and tfdA were both present prior to amendment at levels of ~5 × 104 and ~ 10² copies g⁻¹ soil, respectively, and both reached over 105copies g⁻¹ soil. While expression of all three target genes was detected during two cycles of herbicide degradation, a time-shift occurred between maximum expression of each gene. Gene diversity by denaturing gradient gel electrophoresis (DGGE) uncovered a diversity of sdpA and tfdA genes at the DNA level while rdpA remained highly conserved. However, mRNA profiles indicated that all transcribed tfdA sequences were class III genes while rdpA transcripts shared 100% identity to rdpA of Delftia acidovorans MC1 and sdpA transcripts shared 100% identity to sdpA from Sphingomonas herbicidovorans MH. This is the first report to describe expression dynamics of multiple α-KG dioxygenase-encoding genes in the indigenous microbial community as related to degradation of a phenoxypropionate herbicide in soil.

Recurrent vascular catheter-related bacteremia caused by Delftia acidovorans with different antimicrobial susceptibility profiles.

An 11-year-old girl with metastatic neuroblastoma developed recurrent bacteremia during sustained neutropenia after autologous peripheral blood transplantation. All febrile episodes of bacteremia were caused by single Delftia acidovorans strain revealed by ERIC-PCR. This strain became resistant to broad-spectrum penicillins and cephalosporins through antibiotic treatments. Removal of the indwelling vascular catheter resulted in resolution of the infection. So far as we know, this is the first report of vascular catheter-related D. acidovorans bacteremia in Japan.

Chain transfer reaction catalyzed by various polyhydroxyalkanoate synthases with poly(ethylene glycol) as an exogenous chain transfer agent.

Polyhydroxyalkanoate (PHA) synthases catalyze chain transfer (CT) reaction after polymerization reaction of PHA by transferring PHA chain from PHA synthase to a CT agent, resulting in covalent bonding of CT agent to PHA chain at the carboxyl end. Previous studies have shown that poly(ethylene glycol) (PEG) is an effective exogenous CT agent. This study aimed to compare the effects of PEG on CT reaction during poly[(R)-3-hydroxybutyrate] [P(3HB)] synthesis by using six PHA synthases in Escherichia coli JM109. The synthesized P(3HB) polymers were characterized in terms of molecular weight and end-group structure. Supplementation of PEG to the culture medium reduced P(3HB) molecular weights by up to 96% due to PEG-induced CT reaction. The P(3HB) polymers were subjected to (1)H NMR analysis to confirm the formation of a covalent bond between PEG and P(3HB) chain at the carboxyl end. This study revealed the reactivity of PHA synthases to PEG with respect to CT reaction in E. coli.

Abundance and expression of enantioselective rdpA and sdpA dioxygenase genes during degradation of the racemic herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate in soil.

The rdpA and sdpA genes encode two enantioselective alpha-ketoglutarate-dependent dioxygenases catalyzing the initial step of microbial degradation of the chiral herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate (R,S-dichlorprop). Primers were designed to assess abundance and transcription dynamics of rdpA and sdpA genes in a natural agricultural soil. No indigenous rdpA genes were detected, but sdpA genes were present at levels of approximately 10(3) copies g of soil(-1). Cloning and sequencing of partial sdpA genes revealed a high diversity within the natural sdpA gene pool that could be divided into four clusters by phylogenetic analysis. BLASTp analysis of deduced amino acids revealed that members of cluster I shared 68 to 69% identity, cluster II shared 78 to 85% identity, cluster III shared 58 to 64% identity, and cluster IV shared 55% identity to their closest SdpA relative in GenBank. Expression of rdpA and sdpA in Delftia acidovorans MC1 inoculated in soil was monitored by reverse transcription quantitative real-time PCR (qPCR) during in situ degradation of 2 and 50 mg kg(-1) of (R,S)-dichlorprop. (R,S)-Dichlorprop amendment created a clear upregulation of both rdpA and sdpA gene expression during the active phase of (14)C-labeled (R,S)-dichlorprop mineralization, particularly following the second dose of 50 mg kg(-1) herbicide. Expression of both genes was maintained at a low constitutive level in nonamended soil microcosms. This study is the first to report the presence of indigenous sdpA genes recovered directly from natural soil and also comprises the first investigation into the transcription dynamics of two enantioselective dioxygenase genes during the in situ degradation of the herbicide (R,S)-dichlorprop in soil.

Uptake kinetics of 2,4-dichlorophenoxyacetate by Delftia acidovorans MC1 and derivative strains: complex characteristics in response to pH and growth substrate.

The present investigation showed that active processes were involved in the uptake of 2,4-dichlorophenoxyacetate (2,4-D) by Delftia acidovorans MC1. With 2,4-D-grown cells, uptake at pH 6.8 was highly affine and showed a complex pattern-forming intermediary plateau at 20-100 microM 2,4-D. The kinetics became increasingly sigmoidal with raising of the pH to 7.5 and 8.5, and complexity disappeared. The apparent maximum was obtained at around 400 microM 2,4-D at either pH, and amounted to 15-20 nmol/min x mg protein. Higher substrate concentrations resulted in significant inhibition. With cells grown on (RS)-2-(2,4-dichlorophenoxy)propionate, 2,4-D uptake increased significantly and reached 45 nmol/min x mg, hinting at induction of a specific carrier(s). The kinetic characteristics made it apparent that several proteins contribute to 2,4-D uptake in MC1. An open reading frame was detected which has similarity to genes encoding major facilitator superfamily (MFS) transporters. Mutant strains that lacked this gene showed altered kinetics with decreased affinity to 2,4-D at pH 6.8. A mutant with complete deficiency in phenoxyalkanoate utilization showed an almost linear uptake pattern hinting at sole diffusion. Cloning of tfdK encoding a specific transporter for 2,4-D resulted in an increased uptake rate and, above all, higher affinity at slightly alkaline conditions due to hyperbolic kinetics. The presence of carbonylcyanide m-chlorophenylhydrazone led to the subsequent strong inhibition of 2,4-D uptake, suggesting proton symport as the likely active mechanism.

2,4-Dichlorophenoxyacetic acid (2,4-D) utilization by Delftia acidovorans MC1 at alkaline pH and in the presence of dichlorprop is improved by introduction of the tfdK gene.

Growth of Delftia acidovorans MC1 on 2,4-dichlorophenoxyacetic acid (2,4-D) and on racemic 2-(2,4-dichlorophenoxy)propanoic acid ((RS)-2,4-DP) was studied in the perspective of an extension of the strain's degradation capacity at alkaline pH. At pH 6.8 the strain grew on 2,4-D at a maximum rate (mu max) of 0.158 h(-1). The half-maximum rate-associated substrate concentration (Ks) was 45 microM. At pH 8.5 mu max was only 0.05 h(-1) and the substrate affinity was mucher lower than at pH 6.8. The initial attack of 2,4-D was not the limiting step at pH 8.5 as was seen from high dioxygenase activity in cells grown at this pH. High stationary 2,4-D concentrations and the fact that mu max with dichlorprop was around 0.2 h(-1) at both pHs rather pointed at limited 2,4-D uptake at pH 8.5. Introduction of tfdK from D. acidovorans P4a by conjugation, coding for a 2,4-D-specific transporter resulted in improved growth on 2,4-D at pH 8.5 with mu max of 0.147 h(-1) and Ks of 267 microM. Experiments with labeled substrates showed significantly enhanced 2,4-D uptake by the transconjugant TK62. This is taken as an indication of expression of the tfdK gene and proper function of the transporter. The uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP) reduced the influx of 2,4-D. At a concentration of 195 microM 2,4-D, the effect amounted to 90% and 50%, respectively, with TK62 and MC1. Cloning of tfdK also improved the utilization of 2,4-D in the presence of (RS)-2,4-DP. Simultaneous and almost complete degradation of both compounds occurred in TK62 up to D = 0.23 h(-1) at pH 6.8 and up to D = 0.2 h(-1) at pH 8.5. In contrast, MC1 left 2,4-D largely unutilized even at low dilution rates when growing on herbicide mixtures at pH 8.5.

Purification, characterization, gene cloning and nucleotide sequencing of D: -stereospecific amino acid amidase from soil bacterium: Delftia acidovorans.

The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40 degrees C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45 degrees C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd2+, Ag+, Zn2+, Hg2+ and As3+ . The NH2 terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.

Genes involved in aniline degradation by Delftia acidovorans strain 7N and its distribution in the natural environment.

Aniline-degraders were isolated from activated sludge and environmental samples and classified into eight phylogenetic groups. Seven groups were classified into Gram-negative bacteria, such as Acidovorax sp., Acinetobacter sp., Delftia sp., Comamonas sp., and Pseudomonas sp., suggesting the possible dominance of Gram-negative aniline-degraders in the environment. Aniline degradative genes were cloned from D. acidovorans strain 7N, and the nucleotide sequence of the 8,039-bp fragment containing eight open reading frames was determined. Their deduced amino acid sequences showed homologies to glutamine synthetase (GS)-like protein, glutamine amidotransferase (GA)-like protein, large and small subunits of aniline dioxygenase, reductase, LysR-type regulator, small ferredoxin-like protein, and catechol 2,3-dioxygenase, suggesting a high similarity of this gene cluster to those in P. putida strain UCC22 and Acinetobacter sp. strain YAA. Polymerase chain reaction (PCR) and sequencing analyses of GS-like protein gene segments of other Gram-negative bacteria suggested that Gram-negative bacteria have aniline degradative gene that can be divided into two distinctive groups.

Localization and characterization of two novel genes encoding stereospecific dioxygenases catalyzing 2(2,4-dichlorophenoxy)propionate cleavage in Delftia acidovorans MC1.

Two novel genes, rdpA and sdpA, encoding the enantiospecific alpha-ketoglutarate dependent dioxygenases catalyzing R,S-dichlorprop cleavage in Delftia acidovorans MC1 were identified. Significant similarities to other known genes were not detected, but their deduced amino acid sequences were similar to those of other alpha-ketoglutarate dioxygenases. RdpA showed 35% identity with TauD of Pseudomonas aeruginosa, and SdpA showed 37% identity with TfdA of Ralstonia eutropha JMP134. The functionally important amino acid sequence motif HX(D/E)X(23-26)(T/S)X(114-183)HX(10-13)R/K, which is highly conserved in group II alpha-ketoglutarate-dependent dioxygenases, was present in both dichlorprop-cleaving enzymes. Transposon mutagenesis of rdpA inactivated R-dichlorprop cleavage, indicating that it was a single-copy gene. Both rdpA and sdpA were located on the plasmid pMC1 that also carries the lower pathway genes. Sequencing of a 25.8-kb fragment showed that the dioxygenase genes were separated by a 13.6-kb region mainly comprising a Tn501-like transposon. Furthermore, two copies of a sequence similar to IS91-like elements were identified. Hybridization studies comparing the wild-type plasmid and that of the mutant unable to cleave dichlorprop showed that rdpA and sdpA were deleted, whereas the lower pathway genes were unaffected, and that deletion may be caused by genetic rearrangements of the IS91-like elements. Two other dichlorprop-degrading bacterial strains, Rhodoferax sp. strain P230 and Sphingobium herbicidovorans MH, were shown to carry rdpA genes of high similarity to rdpA from strain MC1, but sdpA was not detected. This suggested that rdpA gene products are involved in the degradation of R-dichlorprop in these strains.

An extra large insertion in the polyhydroxyalkanoate synthase from Delftia acidovorans DS-17: its deletion effects and relation to cellular proteolysis.

The polyhydroxyalkanoate (PHA) synthase (PhaC(Da)) from Delftia acidovorans DS-17 (formerly Comamonas acidovorans) has a unique large insertion consisting of 40 amino acid residues in the alpha/beta hydrolase fold region. In order to examine whether this insertion is necessary for enzyme function, we generated a mutant gene where the nucleotides encoding the insertion sequence were deleted [phaC(Da)del(342-381)]. The ability of the mutant PhaC(Da) lacking the insertion sequence to produce PHA in recombinant Escherichia coli JM109 was compared with that of wild-type PhaC(Da). The results revealed that the mutant enzyme had approximately one fourth the activity of the wild-type enzyme. However, there was no significant difference in PHA content accumulated in cells harboring either the mutant PhaC(Da) or wild-type PhaC(Da) nor were there any differences in the molecular masses of the produced polymers. Therefore, we have concluded that the characteristic insertion is not indispensable for PHA synthesis. Also, slight cellular proteolysis in E. coli was found specifically for wild-type PhaC(Da) by Western blot analysis. This result prompted us to further examine the proteolytic stability of PhaC(Da) in D. acidovorans. Consequently, it has been suggested that the insertion region of PhaC(Da) is susceptible to cellular proteolysis during accumulation of PHA.