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Open Access Research article

Physiology of deletion mutants in the anaerobic β-myrcene degradation pathway in Castellaniella defragrans

Frauke Lüddeke, Aytac Dikfidan and Jens Harder*

Author Affiliations

Dep. of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany

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BMC Microbiology 2012, 12:192  doi:10.1186/1471-2180-12-192

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2180/12/192


Received:20 February 2012
Accepted:21 August 2012
Published:4 September 2012

© 2012 Lüddeke et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

Monoterpenes present a large and versatile group of unsaturated hydrocarbons of plant origin with widespread use in the fragrance as well as food industry. The anaerobic β-myrcene degradation pathway in Castellaniella defragrans strain 65Phen differs from well known aerobic, monooxygenase-containing pathways. The initial enzyme linalool dehydratase-isomerase ldi/LDI catalyzes the hydration of β-myrcene to (S)-(+)-linalool and its isomerization to geraniol. A high-affinity geraniol dehydrogenase geoA/GeDH and a geranial dehydrogenase geoB/GaDH contribute to the formation of geranic acid.

A genetic system was for the first time applied for the betaproteobacterium to prove in vivo the relevance of the linalool dehydratase-isomerase and the geraniol dehydrogenase. In-frame deletion cassettes were introduced by conjugation and two homologous recombination events.

Results

Polar effects were absent in the in-frame deletion mutants C. defragrans Δldi and C. defragrans ΔgeoA. The physiological characterization of the strains demonstrated a requirement of the linalool dehydratase-isomerase for growth on acyclic monoterpenes, but not on cyclic monoterpenes. The deletion of geoA resulted in a phenotype with hampered growth rate on monoterpenes as sole carbon and energy source as well as reduced biomass yields. Enzyme assays revealed the presence of a second geraniol dehydrogenase. The deletion mutants were in trans complemented with the broad-host range expression vector pBBR1MCS-4ldi and pBBR1MCS-2geoA, restoring in both cases the wild type phenotype.

Conclusions

In-frame deletion mutants of genes in the anaerobic β-myrcene degradation revealed novel insights in the in vivo function. The deletion of a high-affinity geraniol dehydrogenase hampered, but did not preclude growth on monoterpenes. A second geraniol dehydrogenase activity was present that contributes to the β-myrcene degradation pathway. Growth on cyclic monoterpenes independent of the initial enzyme LDI suggests the presence of a second enzyme system activating unsaturated hydrocarbons.

Keywords:
β-myrcene; phellandrene; Anaerobic degradation; Geraniol dehydrogenase; Linalool dehydratase-isomerase; Genetic system

Background

Monoterpenes represent a prominent group of volatile organic compounds (VOC), with an estimated mean global emission of 117 Tg C yr-1 into the atmosphere [1] and a fast photochemical turnover [2]. Especially coniferous plants are considered to be main producers of monoterpenes, e.g. for thermotolerance or for communication between plants or the interaction between plants and insects [3-5]. Monoterpenes also enter the soil by the rhizosphere or by rotten leafs [6], where they inhibit growth of microorganisms as well as of seedlings [7-9], but also stimulate the bacterial activity detectable in higher biomass and CO2-production [5,10,11]. By definition, monoterpenes possess a carbon skeleton based on two C5 units originating from isopentenyl pyrophosphate (IPP), which is synthesized via the mevalonate (in eukaryotes) or the mevalonate-independent pathway (in prokaryotes and plant plastids) [12-14]. Mainly, plant monoterpenes are produced via the latter pathway, but the metabolic cross linkage between both has been reported in several species [15,16].

Monoterpenes are together with sesquiterpenes the major constituents of essential oils. Due to their status – they are generally recognized as safe (GRAS) [17] - and their odorous properties, these substances are widespread in the food, cosmetics, flavour and fragrance industry [18]. Monoterpenes are utilized as energy and carbon source by several aerobic microorganisms, a fact known since the 1960s [19-21]. Most reports dealt with Pseudomonas species, e.g. [22-28], but also Bacillus stearothermophilus[29], Rhodococcus erythropolis[30], and Enterobacter cowanii[31] metabolize these hydrocarbons. The microbial degradation of α-pinene and limonene, one of the most widespread monoterpenes in nature, involve complex and multiple pathways that comprise in large part oxidation reactions [30,32-34]. In addition these studies revealed the importance of oxygenases, which catalyze hydroxylation reactions with molecular oxygen as co-substrate [35-38].

Under anaerobic conditions, the biochemistry for the activation of these natural abundant alkenes seems to follow a totally different mechanism. The first evidence for the anaerobic degradation of monoterpenes were seven nitrate-reducing enrichment cultures with monoterpenes as sole carbon source [39]. Isolation led to the description of four Alcaligenes defragrans strains, including strain 65Phen isolated with α-phellandrene [40]. A taxonomic study transferred these strains in the novel genus Castellaniella within the Alcaligenaceae, as C. defragrans[41]. The betaproteobacterium is capable of degrading a broad substrate range of a-, mono-, and bicyclic monoterpenes (Figure  1) [40]. Initial metabolite studies on the anaerobic monoterpene degradation pathway in C. defragrans elucidated the demand for a sp2-hybridized C1-atom as structural prerequisite for monoterpenes utilization [42] as well as the formation of geranic acid as intermediate [43], which is likely degraded on a modified β-oxidation pathway [44,45]. These findings proposed the degradation of β-myrcene via hydration to linalool, followed by isomerisation to geraniol, and then two oxidations to geranial and to geranic acid [43]. The genes and proteins involved this pathway were recently identified [46,47] (Figure  2). The bifunctional linalool dehydratase-isomerase ldi/LDI catalyzes the first two steps, the highly enantiospecific hydration of β-myrcene to (S)-(+)-linalool and its isomerisation to geraniol [46,48]. Subsequently, two dehydrogenases oxidize the allylalcohol geraniol and geranial. The geraniol dehydrogenase geoA/GeDH (E. C. 1.1.1.183) is a member of the medium-chain dehydrogenase/reductase superfamily [49] with high affinity for its substrate geraniol [47]. In vitro studies confirmed the activity of a geranial dehydrogenase geoB/GaDH. Both dehydrogenases were expressed in cells growing with monoterpenes [47].

thumbnailFigure 1. Monoterpene substrate range ofC. defragrans [40].

thumbnailFigure 2. Anaerobic degradation pathway of β-myrcene byC. defragrans. Anaerobic β-myrcene degradation in C. defragrans 65Phen. I, β-myrcene (7-methyl-3-methylen-1,6-octadien); II, (S)-(+)-linalool; III, geraniol ((2E)-3,7-dimethyl-2,6-octadien-1-ol); IV, geranial ((2E)-3,7-dimethyl-2,6-octadien-1-al); V, geranic acid ((2E)-3,7-dimethyl-2,6-octadienoic acid). LDI, linalool dehydratase-isomerase; GeDH, geraniol dehydrogenase; GaDH, geranial dehydrogenase.

So far, the evidence for the anaerobic β-myrcene degradation pathway was rather biochemically based on metabolite and enzyme studies. To prove the physiological role in vivo, we created deletion mutants of C. defragrans missing the gene ldi and geoA, respectively. The previous findings, i.e. the geranic acid formation and the induced dehydrogenase activities, were observed in both acyclic and monocyclic monoterpenes grown cells and suggested the existence of a common degradation pathway. To clarify whether there is one defined metabolic route or multiple pathways present for the anaerobic degradation of monoterpenes in C. defragrans, we deleted the initial, β-myrcene-activating enzyme, the LDI. The deletion of the GeDH was of interest due to the frequent presence of multiple alcohol dehydrogenases in genomes, often with a broad substrate range.

Results and Discussion

Construction of the in-frame deletion mutant C. defragrans Δldi and ΔgeoA

Growth of C. defragrans as single colony under denitrifying conditions was achieved on acetate in a defined, solidified medium. A spontaneous mutant strain resistant to rifampicin (150 μg/ml) was obtained showing the phenotype of the wildtype with respect to growth on monoterpenes (Additional file 1: Table S1). Conjugation was established with the broad host range plasmid pBBR1MCS-2, proceeding with a frequency of 1.8 × 10-4 transconjugants cell/ donor cells in 8 h (Additional file 1: Table S2). The plasmid was maintained in C. defragrans. For genomic deletion mutants, we constructed pK19mobsacBΔldi and pK19mobsacBΔgeoA that carried the start and stop codon of the ldi (ORF26) or geoA (ORF31) separated by a specific restriction site and the upstream and downstream located regions (Additional file 1: Figure S1). The sequence information was obtained from a 50 kb contig (Acc. no. FR669447.2) with the following annotation for ORFs adjacent to ldi or geoA: ORF27 as a thioesterase, ORF29 as a putative subunit of cytochrome c oxidase, ORF30 as a secretory protein and ORF32 as a long-chain-fatty-acid CoA ligase, while for ORF25 only hypothetical proteins were found in database queries (Additional file 1: Figure S 1). Conjugation and homologous recombination yielded genomic in-frame deletions, with a second recombination frequency of 0.5% and 1.25% for the deletion of ldi and of geoA, respectively. Analysis by PCR revealed in the deletion mutants the expected, shortened amplicons with primer pairs spanning the deleted gene in comparison with the wild type (Additional file 1: Figure S3). Polar effects due to the deletion of ldi or geoA were not detected in mRNA analyses (Additional file 1: Figure S4). The genes ldi or geoA and their native ribosomal binding site were cloned in the MCS of pBBR1MCS plasmids. Conjugation into C. defragrans deletion mutants yielded ampicillin-resistant transconjugants named C. defragrans Δldicomp and kanamycin-resistant transconjugants named C. defragrans ΔgeoAcomp.

Additional file 1. Additional Material.

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Physiological characterization of C. defragrans Δldi

Under standard culturing conditions for anaerobic, denitrifying growth with 10 mM nitrate and 4 mM cyclic α-phellandrene or limonene in 2,2,4,6,6,8,8-heptamethylnonane (HMN), C. defragrans strains 65Phen, Δldi, and Δldicomp grew to final OD ranging from 0.25 to 0.35 (Figure  3A, B). C. defragrans strains 65Phen metabolized the acyclic β-myrcene, but C. defragrans Δldi lacking the gene for the ldi failed to grow with this substrate (Figure  3C). The in trans complementation Δldicomp restored the wild type phenotype. These data showed that the LDI is essential for the metabolism of β-myrcene, but not for the cyclic monoterpenes α-phellandrene and limonene.

thumbnailFigure 3. Time courses of anaerobic denitrifying growth of C .defragrans mutant strains. Time courses of anaerobic, denitrifying growth of C. defragrans strains 65Phen (●), Δldi (□), Δldicomp (■), ΔgeoA (▵) and ΔgeoAcomp (▴) on different carbon sources, namely (A) 4 mM α-phellandrene, (B) 4 mM limonene, and (C) 4 mM β-myrcene. Negative controls without inoculum or without substrate did not show an increase in turbidity (data not shown).

In previous studies, β-myrcene as well as α-phellandrene supported the formation of geranic acid in cell suspension experiments. The geranic acid pool was 10fold larger in β-myrcene experiments than with the cyclic monoterpenes α-pinene, α-phellandrene, and limonene [43]. We assayed the geranic acid pools in C. defragrans mutant strains under nitrate-limited conditions in liquid cultures on 6 mM monoterpene in HMN (Table  1). This metabolite was only detectable in myrcene-grown C. defragrans cultures with the ldi either present in the genome or in trans, in concentrations of 8.85 μM and 6.61 μM, respectively. In α-phellandrene grown cultures, geranic acid was detectable in media of these C. defragrans strains in concentrations of 0.24 μM and 0.33 μM. Geranic acid formation was not detectable in cultures of the mutant lacking the gene ldi. The RP-HPLC detection limit was 6.4 nM, thus geranic acid formation in C. defragrans Δldi was below a thousandth of that in the wild type. Growth on α-phellandrene clearly does not involve the formation of geranic acid suggesting the presence of another monoterpene degrading pathway that circumvents the activation of the substrate by LDI as well as geranic acid formation.

Table 1. Geranic acid pools in cultivation media

Under aerobic conditions microbial biotransformation of (−)-limonene and β-myrcene revealed the formation of enantiopure (−)-perillyl alcohol, perillyl acid and myrcenic acid [30,50-52]. Anaerobic hydroxylations catalyzed by molybdenum enzymes have been recently reported, e.g. the hydroxylation of ethylbenzene to (S)-phenylethanol in Aromatoleum aromaticum[53] and of cholesterol to cholest-1,4-diene-3-one in Sterolibacterium denitrificans[54]. Whether the degradation of cyclic monoterpenes proceeds via a homologue pathway is subjected in ongoing research. To our knowledge, this is the first report on the existence of different activation mechanisms for cyclic and acyclic monoterpenes in one bacterial strain.

Physiological and enzymatic characterization of C. defragrans ΔgeoA

The deletion of geoA resulted in an increased generation time and reduced biomass yields, e.g. on α-phellandrene, limonene and β-myrcene (Figure  3A-C, Table  2). Nitrate was completely consumed, but the generation time was always prolonged, e.g. 3.5-fold for α-phellandrene. The biomass formed as determined by protein analyses was decreased by 32% to 48% in the deletion mutant (Table  2). Most likely, geraniol was oxidized at slower rate in the deletion mutant. This seems to have an inhibitory effect on the growth due to the known geraniol in vivo toxicity of above 5 μM in the aqueous phase [47]. The intracellular geraniol concentrations were below the detection threshold of gas chromatographical analysis, but we observed physiological evidence for increased geraniol pools. In the cultivation system with HMN, 4 mM geraniol stopped monoterpene utilization completely [47]. In the wild type, addition of 16 mM acetate supported growth in the presence of 4 mM geraniol and 20 mM nitrate to an OD660 of 0.15 (± 0.002; n = 2). The deletion mutant C. defragans ΔgeoA also grew after acetate addition, but reached only an OD660 of 0.061 (± 0.01; n = 2), although both strains consumed the same nitrate amount. In conclusion, C. defragans ΔgeoA reacts more sensitive towards geraniol than the wild type.

Table 2. Physiological properties of C. defragrans strains growing with different monoterpenes

The growth phenotype of the wild type was recovered in the mutant strain by complementation with the geoA gene located on a broad-host range plasmid. The in trans complemented mutant C. defragrans ΔgeoAcomp revealed physiological characteristics similar to C. defragrans 65Phen: growth rate and yield, monoterpene consumption and nitrate reduction were almost identical suggesting that the wild type phenotype was restored by GeDH constitutively expressed from the plasmid pBBR1MCS-2geoA (Table  2, Figure  3).

The absence of GeDH was expected to reduce the rate of geranic acid formation. In this study, geranic acid was detected in cultures grown on 6 mM monoterpene in the presence of HMN and 10 mM nitrate (Table  1). Cultures were sampled after nitrate depletion. Geranic acid concentrations of acidified and lysed cultures were 9 ± 1 μM in the medium of the wild type and 12 ± 1 μM in the medium of the complemented mutant, but only 5 ± 2 μM in the medium of C. defragrans ΔgeoA, thus revealing a limited capacity to form geranic acid in the absence of GeDH.

The ΔgeoA phenotype has still the capacity to degrade monoterpenes, an indication for the presence of another alcohol dehydrogenase that catalyzes the geraniol oxidation. Thus, we tested the GeDH activity spectrophotometrically in cell-free, cytosolic extracts of C. defragrans strains 65Phen, ΔgeoA and ΔgeoAcomp. Under standard conditions, with 0.8 mM geraniol as substrate and identical protein concentrations in the assay, the geraniol oxidation rates were 5.8 nkat mg-1 protein for C. defragrans 65Phen and 1.05 nkat mg-1 protein for C. defragrans ΔgeoA. Complementation restored the activity to 9.4 nkat mg-1 protein in C. defragrans ΔgeoAcomp. The in vivo concentration of geraniol inside the cell is expected to be in the micromolar range [47]. The GeDH activity in the extracts of C. defragrans ΔgeoA catalyzed the reaction with a high affinity, the apparent concentration for half-maximal rate was below 10 μM geraniol (Figure  4). This indicated an activity of the second alcohol dehydrogenase at physiological conditions.

thumbnailFigure 4. Initial specific GeDH activity of C. defragrans strains 65Phen, ΔgeoAand ΔgeoAcomp. The initial specific GeDH activity was measured in triplicates with cytosolic, cell-free extracts of C. defragrans strains 65Phen (□), ΔgeoA (Δ) and ΔgeoAcomp (●). Geraniol concentrations tested were 0, 2, 10, 50, 100 μM.

In summary, the presented data argue for a reduced geraniol flux to geranic acid in the metabolism of the deletion mutant. We suggest that a geraniol accumulation or increased pools of metabolites derived from geraniol on other pathways cause a reduced growth rate as indicated by prolonged generation time, decreased biomass production, and reduced geranic acid formation. The accumulation of a toxic intermediate in monoterpene catabolism causing reduced growth rate has also been seen for deletion mutants of P. putida M1 in ß-myrcene degradation [24,55]. Accumulation of geraniol is known to be toxic for cells: due to its hydrophobic properties it can integrate into bacterial membranes causing disintegrations followed by failure of the proton motive force [56,57].

The presence of several ADHs in a genome is not unusual. In microorganisms, alcohol dehydrogenases possess a wide variety of substrate specificities and are involved in different physiological functions [58]. For various ADHs deficient mutants, retarded growth on the prevailing substrate and reduced ADH activity was observed [59-61]. Also in plants the existence of additional ADHs capable of oxidizing geraniol was suggested [62].

Conclusions

We developed a genetic system for Castellaniella defragrans and constructed in-frame deletion mutants that allows for insights into the physiology of the anaerobic degradation of monoterpenes.

C. defragrans ΔgeoA lacking the gene for a geraniol dehydrogenase was physiologically analysed. The geoA deficient strain exhibited reduced growth on monoterpenes and slower geraniol oxidation rates in soluble extracts, in comparison to the wild type. The original phenotype was restored in trans with an episomal geoA in the C. defragrans ΔgeoAcomp. One explanation for the reduced growth is a higher steady-state level of geraniol in the cell causing toxic effects. These observations together with reduced geranic acid formation demonstrate clearly a participation of GeDH in the anaerobic degradation of β-myrcene. However, the geoA deletion is not mortal. A second GeDH activity is present in soluble extracts. This suggests a need for both GeDHs to balance the geraniol formation by oxidation during fast growth of the wild type.

The physiological characterization regarding growth with acyclic and cyclic monoterpenes exhibited an unexpected effect of the ldi deletion that caused a phenotype dependent on the substrate structure in C. defragrans Δldi: the cyclic monoterpenes α-phellandrene and limonene were metabolized, but not the acyclic β-myrcene. Thus, the degradation of the acyclic β-myrcene required the activity of a linalool dehydratase-isomerase that was not necessary for the degradation of cyclic monoterpenes. This observation indicates for the presence of a second hydrocarbon activating system in C. defragrans.

Methods

Bacterial strains and plasmids

Table  3 described plasmids, C. defragrans strain 65Phen (wild type as well as derivatives) and E. coli strains used in this study. In course of the text, abbreviations are: i) C. defragrans 65Phen-RIF is equivalent to C. defragrans RIF; ii) C. defragrans 65Phen-RIF Δldi is equivalent to C. defragrans Δldi; iii) C. defragrans 65Phen-RIF Δldicomp is equivalent to C. defragrans Δldicomp; iv) C. defragrans 65Phen-RIF ΔgeoA is equivalent to C. defragrans ΔgeoA; v) C. defragrans 65Phen-RIF ΔgeoAcompgeoA is equivalent to C. defragrans ΔgeoAcomp.

Table 3. Strains and plasmids used in this study

Culturing conditions and growth media

E. coli strains were cultured according to established methods [66]. For propagation of plasmids, additional antibiotics were supplemented in the indicated concentrations [66]. Maintenance and growth experiments in liquid cultures with C. defragrans 65Phen and mutants were performed as described previously [40]. Growth in liquid cultures was monitored by turbidity measurements at 660 nm.

Minimal medium for plates contained 50 mM sodium acetate in medium solidified with 18 g/L agar and additionally buffered with 50 mM HEPES, pH 7.2. Incubation took place in anaerobic jars for 4 to 5 days under N2 atmosphere at 28°C. Biomass production of C. defragrans strains was performed according to [46].

Antibiotics were used at following concentrations (unless indicated otherwise): 50 μg/mL ampicillin, 50 μg/mL kanamycin, and 150 μg/mL rifampicin. Plating efficiency was determined by plating decading dilution-to-extinction series of cell suspensions with known optical density (OD) at 660 nm in duplicates.

Preparation and manipulation of genetic material

Genomic DNA was isolated from C. defragrans 65Phen using the DNeasy Tissue Kit (Quiagen, Hilden, Germany). Plasmid DNA was isolated from E. coli strains and C. defragrans 65Phen using mini-plasmid preparation kits (Quiagen). Gel-excised PCR products and plasmid fragments were purified with the QIAquick gel extraction kit (Quiagen).

PCR amplification was usually performed using Taq polymerase (Promega, Madison, USA). For cloning purposes a mixture of Taq polymerase and a thermostable polymerase with proofreading activity (Fermentas, St. Leon Rot, Germany) were applied.

Transcription analyses with Reverse Transcriptase-PCR

Preparation of total RNA from C. defragrans strains after growth on α-pellandrene was performed with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions, followed by cDNA synthesis using the Revert Aid™ First Strand cDNA Synthesis Kit (Fermentas). For transcriptional analyses, RT-PCR was performed with 35 cycles with primer pairs listed in Table  4. Negative controls included RT-PCR without reverse transcriptase. Table  4 lists primers used for the different amplification purposes.

Table 4. Oligonucleotide sequences used in this study

Ligation and transformation of plasmid constructs

Subcloning of PCR products into pCR4-TOPO® vector (Invitrogen, Darmstadt, Germany) was performed corresponding to manufacturer’s instructions. PCR products with inserted restriction sites and purified plasmids were digested with the appropriate restriction enzymes and separated by gel electrophoresis. Both digested plasmids and PCR products were gel excised and purified. For ligation reactions, an insert-vector ratio of 1:1, 3:1 or 10:1 was chosen. To this mixture, T4-ligase buffer (1x), ATP (25 μM) and T4-ligase (2.5 U) were added. Incubation was for 12–16 h at 12°C. Transformation of 5 or 10 μL of the ligation reaction to chemical competent E. coli strains S17-1 or Top10 was performed as described [67]. Single colonies growing on selective solid medium were picked and screened for the correct insert size by PCR applying M13 or T7 primers. Plasmids of positive tested clones were purified and served as sequencing templates.

Construction of suicide plasmids

The 5`- and 3`-flanking regions of ldi or geoA and the start and stop codons of the deleted gene separated by an appropriate specific restriction site were inserted into the suicide vector pK19mobsacB [64]. Oligonucleotide sequences are listed in Table  4.

Initially, the flanking regions were amplified from genomic C. defragrans 65Phen DNA with primers adding restriction enzyme sites to the PCR-product. The 5`-flanking region to the ldi was obtained with the primer pair ORF25_EcoRI_F and ORF25_XhoIATG_R. During amplification of the 3`-flanking region with primer pairs ORF27_XhoI_TAA_F and ORF27_HindIII_R difficulties occurred due to a terminator structure in the genome sequence that was solved with a nested PCR approach. A 2.2 kb amplicon comprising ORF 27 was obtained with the primer pair p27plus_F and p27plus_R that served as template for the initial named primer with an increased initial denaturation time (from 4 min to 10 min). Sequencing of the 763 bp amplicon revealed a base exchange at position 373 from guanine to adenine causing an amino acid replacement from proline to threonine. This shift was revoked by a site directed mutagenesis approach using primer p27_mismatch_F and p27_mismatch_R in combination with ORF27_XhoI_TAA_F and ORF27_HindIII_R, respectively [68]. The particular amplicons were bond to each other in another reaction with the exterior primer pair. The 5`-flanking region of the geoA was obtained with the primer pair ORF2930_XbaI_F & ORF2930_XhoI_R and the geoA 3`-flanking region ORF32_XhoI_F & ORF32_HindIII_R.

The obtained products were subcloned into pCR4-TOPO (Invitrogen, Darmstadt, Germany) and yielded pCR4-ORF25, pCR4-ORF27, pCR4-ORF2930 and pCR4-ORF32. The sequence correctness of these constructs was confirmed by sequencing and restriction digests.

Subcloning vectors were double digested with the prevailing added recognitions site for restriction enzymes. The flanking regions were excised, purified and ligated via a three-piece-ligation into the suicide vector pK19mobsacB [64]. Sequencing of the obtained plasmids pK19mobsacBΔldi and pK19mobsacBΔgeoA was performed to ensure correct sequence of the flanking regions including the start and stop codons of the deleted genes.

Construction of complementation plasmids

For construction of the in trans vector both, the ldi and the geoA was amplified from genomic DNA of C. defragrans 65Phen with primer pair encompassing the entired ORF, i.e. for the ldi primer pair ldi_EcoRI & ldi_BglII, and for geoA geoA_XbaI_F & geoA_HindIII_R (Table  4). Via the added restriction enzyme recognition sites the amplicon was inserted into the multiple cloning site of two different derivatives of the broad-host range vector pBBR1MCS [69]. For confirmation of correct gene insertion the obtained plasmids pBBR1MCS-4ldi and pBBR1MCS-2geoA was sequenced.

Conjugational plasmid transfer

The donor strain, an overnight culture of E. coli S17-1 carrying the appropriate plasmid, and the recipient C. defragrans RIF were grown to late exponential phase and were mixed in several ratios (1:1, 1:5, 1:10) in a total volume of 20 μL and spread as a single drop on minimal agar. After incubation for 24 h at 28°C under oxic conditions the bacteria were resuspended in 1 mL liquid minimal medium. Dilution-to-extinction series were streaked out onto solid minimal medium supplemented with kanamycin and rifampicin and anaerobically incubated at 28°C for four days.

Preparation of cell-free extracts and determination of enzyme activities

Soluble extract preparations of C. defragrans strains 65Phen, ΔgeoA and ΔgeoAcomp were performed as described [46]. The geraniol dehydrogenase activity was monitored in a standard assay following the reduction of NAD+ to NADH at 340 nm as described [47]. Equal total protein amounts were applied as certified in a 200-μl aliquot by the method of Bradford [70] with BSA as standard protein; concentrations were corrected for the unusual high binding of the Coomassie stain to albumin [71].

Chemical analyses of biomass, educts and products

Nitrate and nitrite was measured by HPLC as described by [72]. Based on the fact that protein accounts for 50% of the cell mass, the Bradford assay was applied in duplicates with two different dilutions to determine the total biomass yield [72]. Geranic acid formation was assayed in liquid cultures of C. defragrans strains after confirmed nitrate depletion (Merckoquant® test strips (Merck, Darmstadt, Germany)). 10 mL cell culture was acidified with H3PO4 (final concentration 0.1 M) and extracted with tert-butyl methyl ether in a 1:0.4 ratio (two biological replicates per strain). The ether extract was extracted with 0.1 M NaOH (1:1) and the aqueous phase was subjected twice to reverse-phase HPLC on a Nucleodur® C18 ISIS (4.6 mm × 250 mm, Macherey Nagel, Düren, Germany). Separation of the organic acid was performed with 1 mM H3PO4 in an isocratic water-acetonitrile eluent (45/55 (v/v)) at 1 mL/min and 25°C. Intermediary, the column was cleaned with water-acetonitrile (20/80 (v/v)). UV detection was performed at 215 nm.

Competing interest

The authors declare that they have no competing interests.

Authors' contributions

AD isolated the rifampicin resistant C. defragrans strains and assayed the conjugation frequencies. AD constructed pK19mobsacBΔgeoA and obtained C. defragrans ΔgeoA. FL obtained C. defragrans ΔgeoA and Δldi deletion mutants and constructed the pBBR1MCS-2 derivates. FL performed all the physiological experiments. FL and JH analysed the physiological experiments and wrote the manuscript. All authors read and approved the final manuscript.

Acknowledgements

We thank Robert Marmulla and Maria Grünberg for their technical assistance in the construction of C. defragrans Δldi. This study was financed by the Max Planck Society.

References

  1. Lathiere J, Hauglustaine DA, Friend AD, De Noblet-Ducoudrè N, Viovy N, Folberth GA: Impact of climate variability and land use changes on global biogenic volatile organic compound emissions.

    Atmos Chem Phys 2006, 6:2129-2146. Publisher Full Text OpenURL

  2. Kesselmeier J, Staudt M: Biogenic volatile organic compounds (VOC): an overview on emission, physiology and ecology.

    J Atmos Chem 1999, 33:23-88. Publisher Full Text OpenURL

  3. Dudareva N, Negre F, Nagegowda DA, Orlova I: Plant volatiles: recent advantages and future perspectives.

    Crit Rev Plant Sci 2006, 25:417-440. Publisher Full Text OpenURL

  4. Sharkey TD, Wiberly AE, Donohue AR: Isoprene emission from plants: why and how.

    Ann Bot 2008, 101:5-18. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  5. Smolander A, Ketolab RA, Kotiahod T, Kanervaa S, Suominene K, Kitunena V: Volatile monoterpenes in soil atmosphere under birch and conifers: effects on soil N transformations.

    Soil Biol Biochem 2006, 38:3436-3442. Publisher Full Text OpenURL

  6. Hayward S, Muncey RJ, James AE, Halsall CJ, Hewitt CN: Monoterpene emissions from soil in a Sitka spruce forest.

    Atmos Environ 2001, 35:4081-4087. Publisher Full Text OpenURL

  7. Lin C, Owen SM, Penuelas J: Volatile organic compounds in the roots and rhizosphere of pinus spp.

    Soil Biol Biochem 2007, 39:951-960. Publisher Full Text OpenURL

  8. Ramirez KS, Lauber CL, Fierer N: Microbial consumption and production of volatile organic compounds at the soil-litter interface.

    Biogeochemistry 2010, 99:97-107. Publisher Full Text OpenURL

  9. Vokou D, Douvli P, Blionis GJ, Halley JM: Effects of monoterpenoids, acting alone or in pairs, on seed germination and subsequent seedling growth.

    J Chem Ecol 2003, 29:2281-2301. PubMed Abstract | Publisher Full Text OpenURL

  10. Leff JW, Fierer N: Volatile organic compound (VOC) emissions from soil and litter samples.

    Soil Biol Biochem 2008, 40:1629-1636. Publisher Full Text OpenURL

  11. Vokou D, Chalkos D, Karamanlidou G, Yiangou M: Activation of soil respiration and shift of the microbial population balance in soil as a response to lavendula stoechas essential oil.

    J Chem Ecol 2002, 28:755-768. PubMed Abstract | Publisher Full Text OpenURL

  12. Ajikumar PA, Tyo K, Carlsen S, Mucha O, Phon TH, Stephanopoulos G: Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms.

    Mol Pharm 2008, 5:167-190. PubMed Abstract | Publisher Full Text OpenURL

  13. Flesch G, Rohmer M: Prokaryotic hopanoids: the biosynthesis of the bacteriohopane skeleton - formation of isoprenic units from two distinct acetate pools and a novel type of carbon/carbon linkage between a triterpene and D-ribose.

    Eur J Biochem 1988, 175:405-411. PubMed Abstract | Publisher Full Text OpenURL

  14. Lichtenthaler HK, Rohmer M, Schwender J: Two independent biochemical pathways for isopentenyl diphosphate and isoprenoid biosynthesis in higher plants.

    Physiol Plant 1997, 101:643-652. Publisher Full Text OpenURL

  15. Aharoni A, Giri AP, Deuerlein S, Griepink F, de Kogel WJ, Verstappen FWA, Verhoeven HA, Jongsma MA, Schwab W, Bouwmeester HJ: Terpenoid metabolism in wildtype and transgenic arabidopsis plants.

    Plant Cell 2003, 15:2866-2884. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  16. Hampel D, Mosandl A, Wüst M: Biosynthesis of mono- and sesquiterpenes in carrot roots and leaves (Daucus carota L.): metabolic cross talk of cytosolic mevalonate and plastidial methylerythritol phosphate pathways.

    Phytochemistry 2005, 66:305-311. PubMed Abstract | Publisher Full Text OpenURL

  17. Adams TB, Gavin CL, McGowen MM, Waddell WJ, Cohen SM, Feron VJ, Marnett LJ, Munro IC, Portoghese PS, Rietjens IMCM, Smith RL: The FEMA GRAS assessment of aliphatic and aromatic terpene hydrocarbons used as flavor ingredients.

    Food Chem Toxicol 2011, 49:2471-2494. PubMed Abstract | Publisher Full Text OpenURL

  18. Chen W, Viljoen AM: Geraniol - a review of a commercially important fragrance material.

    S Afr J Bot 2010, 76:643-651. Publisher Full Text OpenURL

  19. Dhavalikar RS, Rangachari PN, Bhattacharyya PK: Microbiological transformations of terpenes. IX. Pathways of degradation of limonene in a soil pseudomonad.

    Indian J Biochem 1966, 3:158-164. PubMed Abstract OpenURL

  20. Seubert W: Degradation of isoprenoid compounds by microorganisms 1. Isolation and characterization of an isoprenoid-degrading bacterium, pseudomonas citronellolis n. sp.

    J Bacteriol 1960, 79:426-434. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  21. Shukla OP, Bhattacharyya PK: Microbiological transformation of terpenes. XI. Pathways of degradation of α- and β-pinenes in a soil pseudomonad (PL-strain).

    Ind J Biochem 1968, 5:92-101. OpenURL

  22. Cantwell SG, Lau EP, Watt DS, Fall R: Biodegradation of acyclic isoprenoids by pseudomonas species.

    J Bacteriol 1978, 135:324-333. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  23. Förster-Fromme K, Höschle B, Mack C, Bott M, Armbruster W, Jendrossek D: Identification of genes and proteins necessary for catabolism of acyclic terpenes and leucine/isovalerate in pseudomonas aeruginosa.

    Appl Environ Microbiol 2006, 72:4819-4828. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  24. Iurescia S, Marconi M, Tofani D, Gambacorta A, Paterno A, Devirgiliis C, van der Werf M, Zennaro E: Identification and sequencing of β-myrcene catabolism genes from pseudomonas sp. strain M1.

    Appl Environ Microbiol 1999, 65:2871-2876. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  25. Madyastha KM, Bhattacharyya PK, Vajdyanathan CS: Metabolism of a monoterpene alcohol, linalool, by a soil pseudomonad.

    Can J Microbiol 1977, 23:230-239. PubMed Abstract | Publisher Full Text OpenURL

  26. Prakash O, Kumari K, Lal R: Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant.

    Int J Syst Evol Microbiol 2007, 57:527-531. PubMed Abstract | Publisher Full Text OpenURL

  27. Tudroszen NJ, Kelly DP, Millis NF: α-Pinene metabolism by pseudomonas putida.

    Biochem J 1977, 168:315-318. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  28. Vandenbergh PA, Wright AM: Plasmid involvement in acyclic isoprenoid metabolism by pseudomonas putida.

    Appl Environ Microbiol 1983, 45:1953-1955. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  29. Chang HC, Oriel PJ: Bioproduction of perillyl alcohol and related monoterpenes by isolates of bacillus stearothermophilus.

    J Food Sci 1994, 59:660-662. Publisher Full Text OpenURL

  30. van der Werf M, Swarts HJ, de Bont JAM: Rhodococcus erythropolis DCL14 contains a novel degradation pathway for limonene.

    Appl Environ Microbiol 1999, 65:2092-2102. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  31. Yang EJ, Park YJ, Chang HC: Cloning of four genes involved in limonene hydroxylation from enterobacter cowanii 6 L.

    J Microbiol Biotechnol 2007, 17:1169-1176. PubMed Abstract | Publisher Full Text OpenURL

  32. Best DJ, Floyd NC, Magalhaes A, Burfield A, Rhodes PM: Initial enzymatic steps in the degradation of α-pinene by pseudomonas fluorescens NCIMB 11671.

    Biocatalysis 1987, 1:147-159. Publisher Full Text OpenURL

  33. Griffiths ET, Bociek SM, Harries PC, Jeffcoat R, Sissons DJ, Trudgill PW: Bacterial metabolism of α-pinene: pathway from α-pinene oxide to acyclic metabolites in nocardia sp. strain P18.3.

    J Bacteriol 1987, 169:4972-4979. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  34. Marostica MR Jr, Pastore GM: Limonene and its oxyfunctionalized compounds: biotransformation by microorganisms and their role as functional bioactive compounds.

    Food Sci Biotechnol 2009, 18:833-841. OpenURL

  35. Linares D, Fontanille P, Larroche C: Exploration of α-pinene degradation pathway of pseudomonas rhodesiae CIP 107491. Application to novalic acid production in a bioreactor.

    Food Res Int 2009, 42:461-469. Publisher Full Text OpenURL

  36. Trudgill PW: Microbial metabolims of monoterpenes – recent developments.

    Biodegradation 1990, 1:93-105. PubMed Abstract | Publisher Full Text OpenURL

  37. Ullah AJH, Murray RI, Bhattacharyya PK, Wagner GC, Gunsalus IC: Protein-components of a cytochrome P-450 linalool 8-methyl hydroxylase.

    J Biol Chem 1990, 265:1345-1351. PubMed Abstract | Publisher Full Text OpenURL

  38. van der Werf MJ, Keijzer PM, van der Schaft PH: Xanthobacter sp C20 contains a novel bioconversion pathway for limonene.

    J Biotechnol 2000, 84:133-143. Publisher Full Text OpenURL

  39. Harder J, Probian C: Microbial degradation of monoterpenes in the absence of molecular oxygen.

    Appl Environ Microbiol 1995, 61:3804-3808. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  40. Foss S, Heyen U, Harder J: Alcaligenes defragrans sp. nov., description of four strains isolated on alkenoic monoterpenes ((+)-menthene, α-pinene, 2-carene, and α-phellandrene) and nitrate.

    Syst Appl Microbiol 1998, 21:237-244. PubMed Abstract | Publisher Full Text OpenURL

  41. Kämpfer P, Denger K, Cook AM, Lee ST, Jäckel U, Denner EBM, Busse HJ: Castellaniella gen. nov., to accommodate the phylogenetic lineage of alcaligenes defragrans, and proposal of castellaniella defragrans gen. nov., comb. nov. and castellaniella denitrificans sp. nov.

    Int J Syst Evol Microbiol 2006, 56:815-819. PubMed Abstract | Publisher Full Text OpenURL

  42. Heyen U, Harder J: Cometabolic isoterpinolene formation from isolimonene by denitrifying alcaligenes defragrans.

    FEMS Microbiol Lett 1998, 169:67-71. Publisher Full Text OpenURL

  43. Heyen U, Harder J: Geranic acid formation, an initial reaction of anaerobic monoterpene metabolism in denitrifying alcaligenes defragrans.

    Appl Environ Microbiol 2000, 66:3004-3009. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  44. Aguilar JA, Zavala AN, Díaz-Pérez C, Cervantes C, Díaz-Pérez AL, Campos-García J: The atu and liu clusters are involved in the catabolic pathways for acyclic monoterpenes and leucine in Pseudomonas aeruginosa.

    Appl Environ Microbiol 2006, 72:2070-2079. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  45. Förster-Fromme K, Jendrossek D: Catabolism of citronellol and related acyclic terpenoids in pseudomonads.

    Appl Microbiol Biotechnol 2010, 87:859-869. PubMed Abstract | Publisher Full Text OpenURL

  46. Brodkorb D, Gottschall M, Marmulla R, Lüddeke F, Harder J: Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes.

    J Biol Chem 2010, 285:30406-30442. OpenURL

  47. Lüddeke F, Wülfing A, Timke M, Germer F, Weber J, Dikfidan A, Rahnfeld T, Linder D, Meyerdierks A, Harder J: Geraniol dehydrogenase and geranial dehydrogenase induced in the anaerobic monoterpene degradation of castellaniella defragrans.

    Appl Environ Microbiol 2012, 78:2128-2136. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  48. Lüddeke F, Harder J: Enantiospecific (S)-(+)-linalool formation from β-myrcene by linalool dehydratase-isomerase.

    Z Naturforsch C Biosci 2011, 66c:409-412. OpenURL

  49. Riveros-Rosas H, Julian-Sanchez A, Villalobos-Molina R, Pardo JP, Pina E: Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily.

    Eur J Biochem 2003, 270:3309-3334. PubMed Abstract | Publisher Full Text OpenURL

  50. Duetz WA, Bouwemeester H, van Beilen JB, Witholt B: Biotransformation of limonene by bacteria, fungi, yeasts, and plants.

    Appl Microbiol Biotechnol 2003, 61:269-277. PubMed Abstract | Publisher Full Text OpenURL

  51. Speelmans G, Bijlsma A, Eggink G: Limonene bioconversion to high concentrations of a single and stable product, perillic acid, by a solvent-resistant pseudomonas putida strain.

    Appl Microbiol Biotechnol 1998, 50:538-544. Publisher Full Text OpenURL

  52. van Beilen JB, Holtackers R, Lüscher D, Bauer U, Witholt B, Duetz WA: Biocatalytic production of perillyl alchohol from limonene using a novel mycobaterium sp. cytochrome P450 alkane hydroxlase expressed in pseudomonas putida.

    Appl Environ Microbiol 2005, 71:173-1744. OpenURL

  53. Kniemeyer O, Heider J: Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme.

    J Biol Chem 2001, 276:21381-21386. PubMed Abstract | Publisher Full Text OpenURL

  54. Chiang YR, Ismail W, Müller M, Fuchs G: Initial steps in the anoxic metabolism of cholesterol by the denitrifying sterolibacterium denitrificans.

    J Biol Chem 2007, 282:13240-13249. PubMed Abstract | Publisher Full Text OpenURL

  55. Santos PM, Sa-Correia I: Adaptation to ß-myrcene catabolism in Pseudomonas sp. M1: an expression proteomic analysis.

    Proteomics 2009, 9:510-5111. OpenURL

  56. Di Pasqua R, Betts G, Hoskins N, Edwards M, Ercolini D, Mauriello G: Membrane toxicity of antimicrobial compounds from essential oils.

    J Agric Food Chem 2007, 55:4863-4870. PubMed Abstract | Publisher Full Text OpenURL

  57. Sikkema J, de Bont JAM, Poolman B: Mechanisms of membrane toxicity of hydrocarbons.

    FEMS Microbiol Rev 1995, 59:201-222. OpenURL

  58. Reid MF, Fewson CA: Molecular characterization of microbial alcohol dehydrogenases.

    Crit Rev Microbiol 1994, 2:13-56. OpenURL

  59. Chattopadhyay A, Förster-Fromme K, Jendrossek D: PQQ-dependent alcohol dehydrogenase (QEDH) of pseudomonas aeruginosa is involved in catabolism of acyclic terpenes.

    J Bas Microbiol 2010, 50:119-124. OpenURL

  60. Malone VF, Chastain AJ, Ohlsson JT, Poneleit LS, Nemecek-Marshall M, Fall R: Characterization of a pseudomonas putida allylic alcohol dehydrogenase induced by growth on 2-methyl-3-buten-2-ol.

    Appl Environ Microbiol 1999, 65:2622-2630. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  61. Sakurai M, Tohda H, Kumagai H, Giga-Hama Y: A distinct type of alcohol dehydrogenase, adh4+, complements ethanol fermentation in an adh1-deficient strain of Schizosaccharomyces pombe.

    FEMS Yeast Res 2004, 4:649-654. PubMed Abstract | Publisher Full Text OpenURL

  62. Iijima Y, Wang G, Fridman E, Pichersky E: Analysis of the enzymatic formation of citral in the glands of sweet basil.

    Arch Biochem Biophys 2006, 448:141-149. PubMed Abstract | Publisher Full Text OpenURL

  63. Simon R, Priefer U, Puhler A: A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria.

    Nat Biotechnol 1983, 1:784-791. Publisher Full Text OpenURL

  64. Schäfer A, Tauch A, Jager W, Kallnowski J, Thierbach G, Pühler A: Small mobilizable multi-purpose cloning vectors derived from the escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of corynebacterium glutamicum.

    Gene 1994, 145:69-73. PubMed Abstract | Publisher Full Text OpenURL

  65. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM, Peterson KM: Four new derivatives of the broad host range cloning vector pBBR1MCS, carrying different antibiotic resistance cassettes.

    Gene 1995, 166:175-176. PubMed Abstract | Publisher Full Text OpenURL

  66. Sambrook J, Russel DW: Molecular cloning: a laboratory manual, ed 3. Cold Spring Harbor: Cold Spring Harbor laboratory Press; 2001. OpenURL

  67. Inoue H, Nojima H, Okayama H: High efficiency transformation of escherichia coli with plasmids.

    Gene 1990, 96:23-28. PubMed Abstract | Publisher Full Text OpenURL

  68. Higuchi R, Krummel B, Saiki RK: A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions.

    Nucleic Acids Res 1988, 16:7351-7367. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  69. Kovach ME, Phillips RW, Elzer PH, Roop RM, Peterson KM: pBBR1MCS: a broad-host-range cloning vector.

    Biotechniques 1994, 16:800-802. PubMed Abstract OpenURL

  70. Bradford MM: A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding.

    Anal Biochem 1976, 72:248-254. PubMed Abstract | Publisher Full Text OpenURL

  71. Biorad: BioRad Protein Assay. Instruction Manual. Munich: BioRad; 1994. OpenURL

  72. Harder J, Probian C: Anaerobic mineralization of cholesterol by a novel type of denitrifying bacterium.

    Arch Microbiol 1997, 167:269-274. PubMed Abstract | Publisher Full Text OpenURL