Acinetobacter Baylyi ADP1 Research Articles

Real-Time monitoring of intracellular wax ester metabolism

BackgroundWax esters are industrially relevant molecules exploited in several applications of oleochemistry and food industry. At the moment, the production processes mostly rely on chemical synthesis from rather expensive starting materials, and therefore solutions are sought from biotechnology. Bacterial wax esters are attractive alternatives, and especially the wax ester metabolism of Acinetobacter sp. has been extensively studied. However, the lack of suitable tools for rapid and simple monitoring of wax ester metabolism in vivo has partly restricted the screening and analyses of potential hosts and optimal conditions.ResultsBased on sensitive and specific detection of intracellular long-chain aldehydes, specific intermediates of wax ester synthesis, bacterial luciferase (LuxAB) was exploited in studying the wax ester metabolism in Acinetobacter baylyi ADP1. Luminescence was detected in the cultivation of the strain producing wax esters, and the changes in signal levels could be linked to corresponding cell growth and wax ester synthesis phases.ConclusionsThe monitoring system showed correlation between wax ester synthesis pattern and luminescent signal. The system shows potential for real-time screening purposes and studies on bacterial wax esters, revealing new aspects to dynamics and role of wax ester metabolism in bacteria.

Exposure of Acinetobacter baylyi ADP1 to the biocide chlorhexidine leads to acquired resistance to the biocide itself and to oxidants

The aim of this study was to determine the effect of exposure to sublethal concentrations of chlorhexidine on oxidative stress protection by Acinetobacter baylyi ADP1. ADP1 cultures were exposed to sublethal concentrations of chlorhexidine prior to being challenged with lethal concentrations of chlorhexidine itself and by oxidants. Oxidant-sensitive dyes and a flow cytometer were used to measure the formation of reactive oxygen species. The role of efflux pumps in chlorhexidine resistance was investigated using a specific inhibitor. Exposure of ADP1 to low concentrations of chlorhexidine induced adaptive and cross-protective responses to chlorhexidine and oxidants (H(2)O(2) and a superoxide anion generator), respectively. Chlorhexidine treatment of ADP1 resulted in the formation of H(2)O(2) and superoxide anions that are probably responsible for the cross-protection against oxidants. Exposure of ADP1 to sublethal concentrations of chlorhexidine confers inducible resistance to lethal concentrations of chlorhexidine itself and to oxidants. An important link was demonstrated between exposure to a biocide and the gaining of resistance to both the biocide and oxidative stress.

Functionalization of whole‐cell bacterial reporters with magnetic nanoparticles

SummaryWe developed a biocompatible and highly efficient approach for functionalization of bacterial cell wall with magnetic nanoparticles (MNPs). Three Acinetobacter baylyi ADP1 chromosomally based bioreporters, which were genetically engineered to express bioluminescence in response to salicylate, toluene/xylene and alkanes, were functionalized with 18 ± 3 nm iron oxide MNPs to acquire magnetic function. The efficiency of MNPs functionalization of Acinetobacter bioreporters was 99.96 ± 0.01%. The MNPs‐functionalized bioreporters (MFBs) can be remotely controlled and collected by an external magnetic field. The MFBs were all viable and functional as good as the native cells in terms of sensitivity, specificity and quantitative response. More importantly, we demonstrated that salicylate sensing MFBs can be applied to sediments and garden soils, and semi‐quantitatively detect salicylate in those samples by discriminably recovering MFBs with a permanent magnet. The magnetically functionalized cells are especially useful to complex environments in which the indigenous cells, particles and impurities may interfere with direct measurement of bioreporter cells and conventional filtration is not applicable to distinguish and harvest bioreporters. The approach described here provides a powerful tool to remotely control and selectively manipulate MNPs‐functionalized cells in water and soils. It would have a potential in the application of environmental microbiology, such as bioremediation enhancement and environment monitoring and assessment.

Biotransformation of glycidol by the unspecific wax ester synthase/acyl‐CoA:diacylglycerol acyltransferase of Acinetobacter baylyi ADP1

AbstractGlycidol was biologically derivatized by the unspecific wax ester synthase/acyl coenzyme A (acyl‐CoA): diacylglycerol acyltransferase (WS/DGAT) from Acinetobacter baylyi ADP1 into glycidyl acyl ester. Catalysis of in vitro conversion of glycidol to glycidyl acyl ester by the WS/DGAT from A. baylyi was verified by (i) a radiometric assay, (ii) thin‐layer chromatography and (iii) also by ESI‐MS. A specific activity of 50 nmol·mg–1·min–1 was obtained when 10 mM glycidol and 5 µM palmitoyl‐CoA were used. In vivo synthesized glycidyl acyl esters in recombinant E. coli were detected and quantified by staining with the epoxide‐specific reagent 4‐(4‐nitrobenzyl)‐pyridine. Of glycidyl acyl esters, 1.5 mg/L was obtained from the culture in the presence of 10 mM glycidol and 10 mM oleate.

Optimization of Bacterial Whole Cell Bioreporters for Toxicity Assay of Environmental Samples

In a study to optimize bacterial whole cell biosensors (bioreporters) for the detection of environmental contaminants, we constructed a toxicity sensing strain Acinetobacter baylyi ADP1_recA_lux. The ADP1_recA_lux is a chromosomally based bioreporter which makes the sensing system stable and negates the need for antibiotics to maintain the trait. The AOP1_recA_lux is activated to express bioluminescence when it is exposed to DNA damaging toxicants. Since the ADP1_recA_lux constantly expresses a baseline level of bioluminescence, false negative results are avoided. The host strain, A. baylyi ADP1, is an ideal model strain typical of water and soil bacteria occurring in the natural environment, and it is more robust than E. coli in terms of viability, maintenance, and storage. The expression of reporter genes - luxCDABE cloned from Photorhabdus luminescens - is robust in a broad range of temperature (10-40 degrees C). The ADP1_recA_lux was used to detect a variety of toxic or potentially toxic compounds including mitomycin C (MMC), methyl methanesulfonate, ethidium bromide, H2O2, toluene, single-wall nanocarbon tubes (SWNCT), nano Au colloids (20 nm), pyrene, beno[a]pyrene, and UV light. These exposures revealed that the ADP1_recA_lux was able to detect both genotoxicity and cytoxicity, qualitatively and quantitatively. The optimal induction time of the ADP1_recA_lux bioreporter was 3 h, and the detection limits for MMC and benezo[a]pyrene were 1.5 nM and 0.4 nM, respectively. The ADP1_recA_lux was also used to detect toxicity of groundwater contaminated by a mixture of phenolic compounds, and the bioreporter toxicity detection was in a good agreement with chemical analysis. The optimized whole cell bioreporter ADP1_recA_lux could be valuable in providing a simple, rapid, stable, quantitative, robust, and costly efficient approach for the detection of toxicity in environmental samples.

Quantitative measurement of pH influence on SalR regulated gene expression in Acinetobacter baylyi ADP1

The influence of medium pH conditions on regulation of the sal operon was quantitatively measured by using a genetically engineered Acinetobacter baylyi ADP1 strain ADPWH_ lux. Live-cell based bioluminescence assays determined that the SalR, a LysR-type transcriptional regulator (LTTR), functioned in a range of medium pH conditions. During exponential growth, SalR regulated bioluminescence production peaked at the neutral pH and tolerated medium pH changes of 5.5–9.0. In the stationary phase, the SalR regulated gene expression reached 20–35% of the maximum productivity during the exponential phase. This report reveals the influence of pH conditions on a LTTR system and demonstrates that the biosensor strain can be a useful tool for understanding transcriptional regulations in different environments.

Structure and substrate specificity of acetyltransferase ACIAD1637 from Acinetobacter baylyi ADP1

Gene ACIAD1637 from Acinetobacter baylyi ADP1 encodes a 182 amino acid putative antibiotic resistance protein. The structure of this protein (termed acepita) has been solved in space group P 2 to 2.35 Å resolution. Acepita belongs to the GCN5-related N-acetyltransferase (GNAT) family, and contains the four sequence motifs conserved among family members. The structure of acepita is compared with that of pita, its homologue from Pseudomonas aeruginosa. Acepita has a similar substrate profile to pita and performs a similar function.

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

BackgroundGenome-scale metabolic models are powerful tools to study global properties of metabolic networks. They provide a way to integrate various types of biological information in a single framework, providing a structured representation of available knowledge on the metabolism of the respective species.ResultsWe reconstructed a constraint-based metabolic model of Acinetobacter baylyi ADP1, a soil bacterium of interest for environmental and biotechnological applications with large-spectrum biodegradation capabilities. Following initial reconstruction from genome annotation and the literature, we iteratively refined the model by comparing its predictions with the results of large-scale experiments: (1) high-throughput growth phenotypes of the wild-type strain on 190 distinct environments, (2) genome-wide gene essentialities from a knockout mutant library, and (3) large-scale growth phenotypes of all mutant strains on 8 minimal media. Out of 1412 predictions, 1262 were initially consistent with our experimental observations. Inconsistencies were systematically examined, leading in 65 cases to model corrections. The predictions of the final version of the model, which included three rounds of refinements, are consistent with the experimental results for (1) 91% of the wild-type growth phenotypes, (2) 94% of the gene essentiality results, and (3) 94% of the mutant growth phenotypes. To facilitate the exploitation of the metabolic model, we provide a web interface allowing online predictions and visualization of results on metabolic maps.ConclusionThe iterative reconstruction procedure led to significant model improvements, showing that genome-wide mutant phenotypes on several media can significantly facilitate the transition from genome annotation to a high-quality model.

New Insights into the Alternative d-Glucarate Degradation Pathway

Although the D-glucarate degradation pathway is well characterized in Escherichia coli, genetic and biochemical information concerning the alternative pathway proposed in Pseudomonas species and Bacillus subtilis remains incomplete. Acinetobacter baylyi ADP1 is a Gram-negative soil bacterium possessing the alternative pathway and able to grow using D-glucarate as the only carbon source. Based on the annotation of its sequenced genome (1), we have constructed a complete collection of singlegene deletion mutants (2). High throughput profiling for growth on a minimal medium containing D-glucarate as the only carbon source for approximately 2450 mutants led to the identification of the genes involved in D-glucarate degradation. Protein purification after recombinant production in E. coli allowed us to reconstitute the enzymatic pathway in vitro. We describe here the kinetic characterization of D-glucarate dehydratase, d-5-keto-4-deoxyglucarate dehydratase, and of cooperative alpha-ketoglutarate semialdehyde dehydrogenase. Transcription and expression analyses of the genes involved in D-glucarate metabolism within a single organism made it possible to access information regarding the regulation of this pathway for the first time.

Bacterial Acyltransferases as an Alternative for Lipase‐Catalyzed Acylation for the Production of Oleochemicals and Fuels

Bacterial acyltransferases are a new class of enzymes, and the first member was identified as WS/DGAT in Acinetobacter baylyi ADP1. Their unspecificity have been used in several biotechnological applications for lipid modification, a field that has been dominated by the use of lipases. Examples are the biosynthesis of jojoba-like wax esters and fatty-acid ethyl esters. In addition, these enzymes are also capable of synthesizing acylthioesters. Acyloxoesters and acylthioesters can thus be produced in vivo by whole-cell fermentations rather than in vitro in an enzyme reactor. In this Minireview, we focus on the biotechnological utilization of acyltransferases for the production of modified lipids from renewable resources.

Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1

Effective gene trapping and screening requires sensory and regulatory compatibility of both host and exogenous systems. The naturally competent bacterium Acinetobacter baylyi ADP1 is able to efficiently take up and integrate exogenous DNA into the chromosome, making it an attractive host system for a wide range of metagenomic applications. To test the ability of A. baylyi ADP1 to express the XylR-regulated Pu promoter from Pseudomonas putida mt-2, we have constructed and examined an A. baylyi ADP1 strain, ADPWH-Pu-lux-xylR. The Pu promoter in ADPWH-Pu-lux-xylR was specifically induced by toluene, m-, p- and o-xylene. The substrate-induced Pu promoter was highly dependent on the growth medium: it was repressed in rich media until stationary phase, but was immediately induced in minimal medium with glucose as the sole carbon source (MMG). However, the Pu promoter was repressed in MMG when it was supplemented with 5 g l(-1) yeast extract. Further investigation showed that the Pu promoter in MMG was repressed by 0.5 g l(-1) aspartic acid or asparagine, but not repressed by glutamine. Changing the carbon/nitrogen ratios by addition of ammonia did not significantly affect the Pu promoter activity but addition of nitrate did. These results show that A. baylyi ADP1 reproduced characteristics of the XylR-regulated Pu promoter observed in its original host. It demonstrates that A. baylyi could provide an excellent genetic host for a wide range of functional metagenomic applications.

A complete collection of single‐gene deletion mutants of Acinetobacter baylyi ADP1

We have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.

Assessment of transformability of bacteria associated with tomato and potato plants

Transformation of plant-associated bacteria by plant DNA has never been demonstrated in agricultural fields. In total 552 bacterial isolates from stems of Ralstonia solanacearum-infected and healthy tomato plants and from stems and leaves of healthy potato plants were tested for natural genetic competence using plasmid pSKTG DNA and homologous DNA extracts. Control strain Acinetobacter baylyi ADP1 was transformable with both DNA extracts. No transformable isolates were observed after treatment with plasmid pSKTG DNA. Two isolates, P34, identified as Pseudomonas trivialis and A19, identified as Pseudomonas fragi, were selected on the basis of the consistently higher Rp-resistant CFU numbers after treatment with DNA from Rp-resistant cells than with that from wild-type cells. P34 showed 2.1-fold and A19 1.5-fold higher Rp-resistant CFU numbers after treatment with DNA from homologous Rp-resistant cells versus that from wild-type cells. It is concluded that bacteria capable of in vitro capture and integration of exogenous DNA into their genomes are relatively rare in culturable bacterial communities associated with tomato and potato plants, or that conditions conducive to transformation were not met in transformation assays.

MaGe: a microbial genome annotation system supported by synteny results

Magnifying Genomes (MaGe) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. Our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions. MaGe is also linked to numerous well-known biological databases and systems. Our system has been thoroughly tested during the annotation of complete bacterial genomes (Acinetobacter baylyi ADP1, Pseudoalteromonas haloplanktis, Frankia alni) and is currently used in the context of several new microbial genome annotation projects. In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at .

Bacterial conversion of D-glucarate to glycerate and pyruvate

Although the d-glucarate degradation pathway is well characterized in Escherichia coli, genetic and biochemical information concerning the alternative pathway proposed in Pseudomonas species and Bacillus subtilis remains incomplete. Acinetobacter baylyi ADP1 is a Gram-negative soil bacterium possessing the alternative pathway and able to grow using d-glucarate as the only carbon source. Based on the annotation of its sequenced genome (1), we have constructed a complete collection of singlegene deletion mutants (2). High throughput profiling for growth on a minimal medium containing d-glucarate as the only carbon source for ∼2450 mutants led to the identification of the genes involved in d-glucarate degradation. Protein purification after recombinant production in E. coli allowed us to reconstitute the enzymatic pathway in vitro. We describe here the kinetic characterization of d-glucarate dehydratase, d-5-keto-4-deoxyglucarate dehydratase, and of cooperative α-ketoglutarate semialdehyde dehydrogenase. Transcription and expression analyses of the genes involved in d-glucarate metabolism within a single organism made it possible to access information regarding the regulation of this pathway for the first time.