DdaR (PA1196) Regulates Expression of Dimethylarginine Dimethylaminohydrolase for the Metabolism of Methylarginines in Pseudomonas aeruginosa PAO1

ABSTRACT

Dimethylarginine dimethylaminohydrolases (DDAHs) catalyze the hydrolysis of methylarginines to yield l-citrulline and methylamines as products. DDAHs and their central roles in methylarginine metabolism have been characterized for eukaryotic cells. While DDAHs are known to exist in some bacteria, including Streptomyces coelicolor and Pseudomonas aeruginosa, the physiological importance and genetic regulation of bacterial DDAHs remain poorly understood. To provide some insight into bacterial methylarginine metabolism, this study focused on identifying the key elements or factors regulating DDAH expression in P. aeruginosa PAO1. First, results revealed that P. aeruginosa can utilize N^G,N^G-dimethyl-l-arginine (ADMA) as a sole source of nitrogen but not carbon. Second, expression of the ddaH gene was observed to be induced in the presence of methylarginines, including N^G-monomethyl-l-arginine (l-NMMA) and ADMA. Third, induction of the ddaH gene was shown to be achieved through a mechanism consisting of the putative enhancer-binding protein PA1196 and the alternative sigma factor RpoN. Both PA1196 and RpoN were essential for the expression of the ddaH gene in response to methylarginines. On the basis of the results of this study, PA1196 was given the name DdaR, for dimethylarginine dimethylaminohydrolase regulator. Interestingly, DdaR and its target ddaH gene are conserved only among P. aeruginosa strains, suggesting that this particular Pseudomonas species has evolved to utilize methylarginines from its environment.

IMPORTANCE Methylated arginine residues are common constituents of eukaryotic proteins. During proteolysis, methylarginines are released in their free forms and become accessible nutrients for bacteria to utilize as growth substrates. In order to have a clearer and better understanding of this process, we explored methylarginine utilization in the metabolically versatile bacterium Pseudomonas aeruginosa PAO1. Our results show that the transcriptional regulator DdaR (PA1196) and the sigma factor RpoN positively regulate expression of dimethylarginine dimethylaminohydrolases (DDAHs) in response to exogenous methylarginines. DDAH is the central enzyme of methylarginine degradation, and its transcriptional regulation by DdaR-RpoN is expected to be conserved among P. aeruginosa strains.

INTRODUCTION

Many eukaryotic proteins are posttranslationally modified through arginine methylation. At the center of this posttranslational modification are enzymes known as protein arginine methyltransferases (PRMTs) that methylate the guanidino nitrogen atoms of arginine residues in S-adenosylmethionine-dependent reactions (1, 2). Because PRMTs have differences in specificity and prevalence, the methylation patterns vary among arginine residues. Consequently, a few methylarginines are known to exist, including N^G-monomethyl-l-arginine (l-NMMA), asymmetric N^G,N^G-dimethyl-l-arginine (ADMA), and symmetric N^G,N^G′-dimethyl-l-arginine (SDMA). During protein turnover or proteolysis, ADMA and l-NMMA are released within the cell in their free forms (3, 4), which allows them to act as competitive inhibitors in arginine utilization pathways (5–7). To circumvent this problem, cells rely on an enzyme called dimethylarginine dimethylaminohydrolase (DDAH) that hydrolyzes l-NMMA and ADMA to generate l-citrulline and either mono- or dimethylamine as end products (3, 8). In contrast, SDMA is not an inhibitor of the arginine utilization pathways, nor is it a substrate for DDAH (8, 9). SDMA is removed from the body through excretion in the urine (4, 10).

The metabolism of methylarginines, especially ADMA, has been extensively studied as it pertains to eukaryotes. Interestingly, genes encoding DDAHs are found in some bacteria, including Mycobacterium tuberculosis, Pseudomonas aeruginosa, Sinorhizobium meliloti, and Streptomyces coelicolor (11). The DDAHs of M. tuberculosis, P. aeruginosa, and S. coelicolor have been biochemically investigated and were shown to catalyze the hydrolysis of both ADMA and l-NMMA (11). The presence of DDAH suggests that these bacteria might be able to utilize methylarginines as a source of carbon and/or nitrogen. As a first step in understanding such metabolism, we sought to identify the genes and regulatory mechanisms necessary for methylarginine utilization in P. aeruginosa PAO1.

DDAH of P. aeruginosa PAO1 has been biochemically characterized (12–15) and is encoded by the PA1195 (ddaH) gene. The ddaH gene has distinguishable features suggesting that it is under the regulation of the alternative sigma factor σ⁵⁴ or RpoN (16, 17). First, located 50 bp upstream of the start codon of ddaH is a putative −24/−12 promoter (Sigma 54 Promoter Database [http://www.sigma54.ca]). The −24/−12 promoter is a highly conserved nucleotide sequence that is recognized by RpoN for transcriptional activation (17, 18). Second, the adjacent PA1196 gene encodes a putative enhancer-binding protein (EBP) with an unknown function (19, 20). EBPs are transcriptional regulators that interact specifically with RpoN to activate transcription from −24/−12 promoters (19, 21, 22). Upon stimulation, EBPs become active and hydrolyze ATP. This nucleotide hydrolysis provides the energy needed for the RpoN-RNA polymerase holoenzyme to transition from a closed to an open complex (21).

In the current study, PA1196 was hypothesized to be a key regulator of ddaH expression in P. aeruginosa PAO1. Specifically, it was proposed that PA1196 in concert with RpoN activates the transcription of ddaH in response to methylarginines, such as ADMA and l-NMMA. The PA1196 gene is in a predicted operon with PA1197, a gene encoding a putative Sir2 protein. Sir2 proteins often function as deacetylases and have regulatory roles in cellular processes, including transcriptional repression or posttranslational modifications (23, 24). It was therefore considered that PA1197 might also have some regulatory role in methylarginine utilization in P. aeruginosa PAO1.

RESULTS

PA1196 is required for utilization of ADMA as a nitrogen source for P. aeruginosa PAO1.

The ddaH, PA1196, and PA1197 genes were deleted from P. aeruginosa PAO1 to create a series of unmarked deletion mutants: the ΔddaH, ΔPA1196, and ΔPA1197 mutants. The mutants and wild-type PAO1 strain were grown in minimal medium supplemented with ADMA as a sole source of either carbon or nitrogen (Fig. 1). As a sole carbon source in the presence of NH₄Cl, ADMA did not support the growth of any of the mutants or PAO1 (Fig. 1A). Cell densities reached a maximum optical density at 600 nm (OD₆₀₀) of ∼0.1 at 48 h postinoculation on ADMA as a carbon source. However, when ADMA served as the sole nitrogen source in the presence of gluconate, slow growth was observed for the ΔPA1197 mutant and PAO1 (Fig. 1B). For these two strains, cell densities reached a maximum OD₆₀₀ of ∼0.6 at 48 h postinoculation on ADMA as a nitrogen source. The ΔddaH and ΔPA1196 mutants exhibited no growth on ADMA as a nitrogen source; cell densities reached a maximum OD₆₀₀ of ∼0.1 (Fig. 1B). Identical growth curves were observed for all strains on l-arginine, l-citrulline, and l-ornithine as nitrogen sources (Fig. 1C to E), suggesting that deletion of ddaH, PA1196, and PA1197 has no effect on the utilization of these compounds. Dimethylamine did not serve as a nitrogen source for any of the mutants or PAO1 (Fig. 1F).

FIG 1.

PA1196 is required for P. aeruginosa PAO1 to grow on ADMA as a nitrogen source. The growth of P. aeruginosa PAO1 and the ΔddaH, ΔPA1196, and ΔPA1197 mutants in minimal medium supplemented with the following nitrogen (10 mM) and carbon (15 mM) sources was measured: NH₄Cl and ADMA (A), ADMA and gluconate (B), l-arginine and gluconate (C), l-citrulline and gluconate (D), l-ornithine and gluconate (E), and dimethylamine and gluconate (F). The strains were grown in 96-well polystyrene plates at 37°C for 24 to 48 h. Data points represent mean values (n = 4), with SDs being <5.0%. Error bars were omitted for clarity.

Expression of either the PA1196 or the ddaH gene from the lac promoter on plasmid pBBR1MCS-5 restored the growth of the ΔPA1196 mutant on ADMA as a nitrogen source (Fig. 2). The finding that plasmid-derived expression of ddaH compensated for the ADMA-related growth deficiency of the ΔPA1196 mutant was an indicator that expression of the ddaH gene is possibly deregulated or insufficient in the absence of the PA1196 gene. Collectively, the results of these growth assays demonstrate that ddaH (as expected) and PA1196 are essential for ADMA utilization in P. aeruginosa PAO1.

FIG 2.

Plasmid-based expression of PA1196 or ddaH rescues the growth of the ΔPA1196 mutant on ADMA. Growth in minimal medium supplemented with 15 mM gluconate, 10 mM ADMA, and 30 μg ml⁻¹ gentamicin was measured for P. aeruginosa PAO1 harboring an empty plasmid (pBBR1MCS-5), the ΔddaH mutant harboring either an empty plasmid (pBBR1MCS-5) or pBRL685 (ddaH⁺), and the ΔPA1196 mutant harboring either an empty plasmid (pBBR1MCS-5), pBRL685 (ddaH⁺), or pBRL686 (PA1196⁺). Note that the ddaH and PA1196 genes were cloned under the control of the lac promoter of pBBR1MCS-5 to generate pBRL685 and pBRL686, respectively. Recombinant strains were grown in 96-well polystyrene plates at 37°C for 48 h. Data points represent mean values (n = 4), with SDs being <5.0%. Error bars were omitted for clarity.

Expression of ddaH is induced by ADMA.

To explore the expression of ddaH, a LacZ reporter was constructed by fusing the ∼500-bp 5′ regulatory region of ddaH with the lacZ open reading frame (ORF) of Escherichia coli. The ddaH::lacZ fusion was cloned into the promoter-less, low-copy-number plasmid ΔPlac-pBBR1MCS-5. Afterwards, P. aeruginosa PAO1 harboring ddaH::lacZ was grown in gluconate-minimal medium to an OD₆₀₀ of 0.3 and then challenged with various substrates, each at a final concentration of 0.1 mM. As shown in Fig. 3A, LacZ activities increased >2-fold at 1.0 h after the addition of ADMA. LacZ activities also increased >2-fold with the addition of l-NMMA, a monomethylated derivative of l-arginine. In contrast, LacZ activities did not change with the addition of l-arginine, l-citrulline, or no substrate.

FIG 3.

Methylarginines induce expression of ddaH::lacZ in P. aeruginosa PAO1. The ∼500-bp 5′ regulatory region of ddaH was fused to E. coli lacZ, and the resulting construct was cloned into a promoter-less plasmid to give ddaH::lacZ. P. aeruginosa PAO1 harboring ddaH::lacZ was grown in gluconate-minimal medium to an OD₆₀₀ of 0.3 and then challenged with either 0.1 mM ADMA, l-NMMA, l-arginine, or l-citrulline (A) or ADMA at various concentrations, 0.001, 0.01, 0.1, or 1.0 mM (B). LacZ activities were measured 1.0 h after the addition of the substrate. Data points represent mean values (n = 3) ± SDs. ANOVA with a Dunnett's post hoc test (α value, 0.05) was done to identify significant differences (P < 0.0001), which are indicated with asterisks.

The effects of various concentrations of exogenous ADMA on the expression of ddaH::lacZ were measured. Final ADMA concentrations of 0.01, 0.1, and 1.0 mM caused LacZ activities to increase >2-fold when ddaH::lacZ was expressed in P. aeruginosa PAO1 (Fig. 3B). The addition of ADMA to 0.001 mM did not significantly affect ddaH::lacZ expression. These results indicate that expression of ddaH in P. aeruginosa PAO1 is inducible by ADMA at relatively low concentrations.

DDAH is regulated by PA1196.

It was next determined what role PA1196 and PA1197 might have on expression of the ddaH gene. Mutants (the ΔddaH, ΔPA1196, and ΔPA1197 mutants) and PAO1 harboring ddaH::lacZ were grown in gluconate-minimal medium to an OD₆₀₀ of 0.3 and then challenged with either no substrate or 0.1 mM ADMA. LacZ activities were subsequently measured at 1.0 h after the addition of the substrate. It was found that the addition of ADMA induced the expression of ddaH::lacZ for both the ΔPA1197 mutant and PAO1; i.e., LacZ activities increased >2-fold for both strains (Fig. 4). For the ΔddaH mutant, LacZ activities increased >7-fold with the addition of ADMA. This elevated fold change compared to the activity observed in PAO1 was expected, because the ΔddaH mutant is unable to catabolize or enzymatically break down ADMA. For the ΔPA1196 mutant, there was no change in LacZ activity with the addition of ADMA. This result is consistent with PA1196 being a positive regulator of the ddaH gene.

FIG 4.

PA1196 is essential for induction of ddaH::lacZ in response to ADMA. Expression of ddaH::lacZ was determined in P. aeruginosa PAO1 and the ΔddaH, ΔPA1196, and ΔPA1197 mutants. Strains harboring ddaH::lacZ were grown in gluconate-minimal medium to an OD₆₀₀ of 0.3 and then challenged with either no substrate or 0.1 mM ADMA. LacZ activities were measured at 1.0 h after the addition of the substrate. Data points represent mean values (n = 3) ± SDs. ANOVA with a Dunnett's post hoc test (α value, 0.05) was done to identify significant differences (P < 0.0001), which are indicated with asterisks.

Deletion of the PA1197 gene did not affect expression of ddaH::lacZ, indicating that PA1197 is not necessary for the transcription of ddaH in response to ADMA. Therefore, it was considered possible that PA1197 regulates the actual function or catalytic activity of DDAH. To address this possibility, cell extracts from mutant and PAO1 strains grown in gluconate-minimal medium were prepared in either the absence or the presence of ADMA. DDAH activity, i.e., the formation of l-citrulline from ADMA, was measured for each cell extract. For all mutant and PAO1 strains grown in the absence of ADMA, the resulting cell extracts yielded DDAH activities of ∼20 U (Fig. 5). However, when the bacteria were grown in the presence of ADMA, DDAH activities were ∼100 U in cell extracts prepared from the ΔPA1197 mutant and PAO1 (Fig. 5). The addition of ADMA caused an ∼5-fold increase in DDAH activity. In contrast, cell extracts prepared from the ΔddaH and ΔPA1196 mutants grown in the presence of ADMA generated DDAH activities of ∼20 U, which was similar to the value measured in the absence of ADMA. These findings confirm that PA1196 is essential for DDAH activity in P. aeruginosa PAO1.

FIG 5.

DDAH activity is dependent on PA1196. P. aeruginosa PAO1 and the ΔddaH, ΔPA1196, and ΔPA1197 mutants were grown in gluconate-minimal medium to an OD₆₀₀ of 0.3 and then challenged with either no substrate or 1.0 mM ADMA. At 2.0 h after the addition of the substrate, cells were collected by centrifugation, washed, and subsequently lysed via sonication. The lysates were cleared of cellular debris, concentrated, and then assayed for DDAH activity, which is reported in units (U), defined as the formation of l-citrulline (nanomoles hour⁻¹ milligram⁻¹ total protein). Data points represent mean values (n = 2) ± SDs. ANOVA with a Dunnett's post hoc test (α value, 0.05) was done to identify significant differences (P < 0.0001), which are indicated with asterisks.

ADMA induces expression of ddaH::lacZ in Pseudomonas putida cells that express PA1196.

Because P. putida KT2440 does not possess any homologs of DDAH or PA1196, it was considered a suitable host to validate the central role of PA1196 in the expression of the ddaH gene. To this end, the PA1196 gene was cloned under the control of the lac promoter on plasmid pBBR1MCS-3, and the resulting plasmid-derived PA1196 was cotransformed with ddaH::lacZ into P. putida KT2440. Recombinant cells were grown in gluconate-minimal medium to an OD₆₀₀ of 0.3 and then challenged with either no substrate or 0.1 mM ADMA. LacZ activities were measured 2.0 h after the addition of the substrate. As shown in Fig. 6, the addition of ADMA induced LacZ activity >20-fold for P. putida KT2440 cells harboring plasmid-derived PA1196 and ddaH::lacZ. PA1196 was essential for this induction, because cells that harbored ddaH::lacZ in combination with either an empty plasmid (pBBR1MCS-3) or a plasmid having PA1196 cloned backwards relative to the orientation of the lac promoter on pBBR1MCS-3 yielded only background levels of LacZ activity with the addition of ADMA.

FIG 6.

PA1196 is essential for induction of ddaH::lacZ in P. putida KT2440. P. putida KT2440 was cotransformed with several plasmid combinations, including (i) ddaH::lacZ and pBRL720 (+PA1196), (ii) ddaH::lacZ and an empty plasmid (pBBR1MCS-3), (iii) ddaH::lacZ and pBRL719 (−PA1196), (iv) ΔPlac-pBBR1MCS-5 and pBRL720 (+PA1196), and (v) empty plasmids (ΔPlac-pBBR1MCS-5 and pBBR1MCS-3). Recombinant strains were grown in gluconate-minimal medium to an OD₆₀₀ of 0.3 and then challenged with either no substrate or 0.1 mM ADMA. LacZ activities were measured at 2.0 h after the addition of the substrate. Note that the PA1196 gene was cloned with either a forward (pBRL720) or a backward (pBRL719) orientation relative to the orientation of the lac promoter of pBBR1MCS-3. Data points represent mean values (n = 3) ± SDs. ANOVA with a Dunnett's post hoc test (α value, 0.05) was done to identify significant differences (P < 0.0001), which are indicated with an asterisk.

RpoN is required for induction of ddaH::lacZ.

A putative RpoN promoter with the sequence TGGCGCGTGGCTTGCA (Sigma 54 Promoter Database [http://www.sigma54.ca]) is located 50 bp upstream of the ddaH ORF. The GG and GC nucleotides (which appear in bold type in the promoter sequence) of the −24 and −12 elements, respectively, are crucial for promoter activity. In order to evaluate the role of this promoter in ddaH expression, the GG nucleotides of the −24 element were replaced with AA in the ddaH::lacZ reporter. As expected, this mutation (−P_RpoN) rendered ddaH::lacZ unresponsive to ADMA in P. aeruginosa PAO1 (Fig. 7). Furthermore, the addition of ADMA did not induce expression of ddaH::lacZ in an rpoN mutant (the rpoN::Ω-Km mutant) of P. aeruginosa PAO1. These findings are in agreement and indicate that expression of ddaH is regulated through RpoN.

FIG 7.

RpoN and its cognate promoter are required for induction of ddaH::lacZ in response to ADMA. Expression of ddaH::lacZ was measured in P. aeruginosa PAO1 and an rpoN mutant (the rpoN::Ω-Km mutant). In addition, expression was measured for a ddaH::lacZ construct that had a mutated RpoN promoter (−P_RpoN); i.e., the conserved GG dinucleotide of the −24 element of the RpoN promoter was changed to AA. Strains harboring the ddaH::lacZ constructs were grown in gluconate-minimal medium supplemented with 1.0 mM l-glutamine to an OD₆₀₀ of 0.3 and then challenged with either no substrate or 0.1 mM ADMA. LacZ activities were measured 1.0 h after the addition of the substrate. Data points represent mean values (n = 3) ± SDs. ANOVA with a Dunnett's post hoc test (α value, 0.05) was done to identify significant differences (P < 0.0001), which are indicated with an asterisk.

ADMA utilization in other strains of P. aeruginosa.

DDAHs and homologs of PA1196 are found in other P. aeruginosa strains (20), which suggests that methylarginine utilization is conserved among them. Indeed, growth on ADMA as a nitrogen source was observed for P. aeruginosa strains PA14 and PAK (Fig. 8A). In comparison, DDAHs are not predicted to occur in other Pseudomonas spp., and consistent with their absence, neither P. putida nor Pseudomonas fluorescens grew on ADMA as a nitrogen source (Fig. 8A). Lastly, we decided to evaluate the growth of P. aeruginosa PAO1 in gluconate-minimal medium supplemented with various concentrations of ADMA. As shown in Fig. 8B, identical growth curves were observed for P. aeruginosa PAO1 on 2.0, 5.0, and 10 mM ADMA. Supplementation with ADMA at 0.2 mM also resulted in detectable growth but at a reduced level compared to that observed for the higher ADMA concentrations.

FIG 8.

ADMA serves as a nitrogen source for other strains of P. aeruginosa. (A) Growth in minimal medium supplemented with 15 mM gluconate and 10 mM ADMA was measured for various P. aeruginosa strains (PAO1, PA14, and PAK), P. putida KT2440, and P. fluorescens ATCC 13525. Strains were grown in 96-well polystyrene plates at 30°C for 72 h. (B) Growth in minimal medium supplemented with 15 mM gluconate and various ADMA concentrations (0.0, 0.2, 2.0, 5.0, and 10 mM) was measured for P. aeruginosa PAO1 in 96-well polystyrene plates at 37°C for 48 h. Data points represent mean values (n = 4), with SDs being <5.0%. Error bars were omitted for clarity.

DISCUSSION

Methylarginine degradation in P. aeruginosa PAO1.

A proposed pathway for the breakdown of methylarginines in P. aeruginosa PAO1 is given in Fig. 9. Extracellular methylarginines are believed to be transported through PA1194 and/or ArcD (PA5170). The PA1194 gene encodes a transport protein exhibiting 60% similarity (49% identity) to ArcD, an l-arginine/l-ornithine antiporter (25, 26). Similar to DDAH and PA1196, homologs of PA1194 exist in other strains of P. aeruginosa. This suggests that PA1194 may have evolved to function as a methylarginine/l-ornithine antiporter. Interestingly, results from the LacZ assays involving P. putida KT2440 (Fig. 6) indicate that this bacterium is capable of the uptake of extracellular ADMA, even though it does not possess a homolog of PA1194. P. putida KT2440 does, however, harbor an l-arginine/l-ornithine antiporter, ArcD (PP_1002), which could be responsible for methylarginine transport in this bacterium. Although PA1194 and ArcD are potentially involved in the transport of methylarginines, further studies are needed to elucidate the actual mechanisms underlying the uptake of methylarginines in P. aeruginosa.

FIG 9.

Proposed pathway for methylarginine degradation in P. aeruginosa PAO1. It is hypothesized that extracellular methylarginines are transported into the bacterium through PA1194 and/or ArcD (PA5170). PA1194 shares 60% similarity (49% identity) with ArcD (PA5170), an l-arginine/l-ornithine antiporter. This suggests that PA1194 might function as a dedicated methylarginine/l-ornithine antiporter. Upon entry, intracellular methylarginines are hydrolyzed into l-citrulline and either mono- or dimethylamine via DDAH (PA1195). Using phosphate as a substrate, ornithine carbamoyltransferase, ArcB (PA5172), catalyzes the conversion of l-citrulline into l-ornithine and carbamoyl phosphate. While the l-ornithine product can be used for the uptake of methylarginines, carbamoyl phosphate is broken down into ATP, CO₂, and NH₃ in a reaction catalyzed by carbamate kinase, ArcC (PA5173).

The central catabolic step in methylarginine utilization is catalyzed by DDAH, which hydrolyzes intracellular methylarginines to generate mono- or dimethylamine and l-citrulline as products. Mono- and dimethylamines have not been reported to be viable nutrients for P. aeruginosa, and in this study, dimethylamine did not serve as a nitrogen source for P. aeruginosa PAO1 (Fig. 1). However, l-citrulline is an intermediate of arginine degradation (the arginine deiminase or ArcABC pathway) and has been shown to be a poor nitrogen source for P. aeruginosa (27–29). On the basis of this information, it is predicted that the l-citrulline product of DDAH catalysis is converted into l-ornithine and carbamoyl phosphate via catabolic ornithine carbamoyltransferase (ArcB) (Fig. 9). Carbamate kinase (ArcC) then transfers the phosphorous group from carbamoyl phosphate onto ADP, thus yielding ATP, CO₂, and NH₃ as products. This series of reactions would account for the ability of P. aeruginosa PAO1 to use ADMA as a nitrogen source, albeit poorly (Fig. 1).

The significance or importance of methylarginine utilization by P. aeruginosa has yet to be established. Data from the literature indicate that there is ∼0.2 to 20 μmol of ADMA per kg of plant tissue (30) and ∼0.01 to 1.0 μmol of ADMA per g of animal protein (31), and plasma concentrations of ADMA are on the order of 0.3 to 0.7 μM in healthy humans (32, 33). These values in combination with the results from this study suggest that P. aeruginosa assimilates exogenous methylarginines to supplement its growth rather than using these compounds as a main source of nitrogen and/or energy. Additionally, l-NMMA and ADMA are inhibitors of nitric oxide (NO) production in eukaryotes (7), so it is possible that methylarginine degradation serves as a protective measure for NO signaling in P. aeruginosa.

DdaR (PA1196) as a regulator of DDAH in P. aeruginosa PAO1.

One of the more significant findings of this study was the identification of the putative EBP PA1196 as an essential regulator of the expression of the ddaH gene in response to methylarginines. Consequently, PA1196 was named DdaR, for dimethylarginine dimethylaminohydrolase regulator. DdaR has a predicted modular structure comprised of an N-terminal sensor domain, a central sigma 54 interaction domain, and a C-terminal DNA-binding domain that possesses a FIS-type helix-turn-helix motif (19, 20). DdaR is not a homolog of any previously characterized EBP and therefore represents a class of EBPs whose regulatory activities are mediated through methylarginines. Homologs of DdaR are found only in the genomes of other strains of P. aeruginosa. DdaR homologs do not occur in other Pseudomonas spp., nor are they found in other bacteria which possess DDAHs. This suggests that the DdaR-RpoN mechanism for regulating expression of ddaH is unique to P. aeruginosa. Despite DDAH and PA1196 being conserved among P. aeruginosa strains, the ability to grow on methylarginines as a sole source of nitrogen varies among them (Fig. 8). The reasons behind this growth variation is unclear but might be related to factors such as the experimental growth temperature, RpoN activity, l-citrulline degradation, and tolerance to dimethylamine.

Apart from ddaH, it is not clear what other genes are regulated by DdaR. The arcBC genes, which are central in l-citrulline degradation, do not possess any putative −24/−12 promoters (Sigma 54 Promoter Database [http://www.sigma54.ca]). Both PA1194 and ArcD (PA5170) are hypothesized to be involved in methylarginine transport, but neither corresponding gene possesses a −24/−12 promoter. The absence of −24/−12 promoters among these genes is a clear indicator that they are not direct targets of transcriptional activation by RpoN. More extensive analyses, e.g., transcriptomic studies, are needed to determine the scope and magnitude of genes whose expression is affected by DdaR.

The function of PA1197 remains unclear.

The ddaR gene is in a putative operon with PA1197, which encodes a Sir2-type deacetylase. While this operon structure would suggest that PA1197 has some role in methylarginine utilization, we found that a ΔPA1197 mutant exhibited wild-type growth on ADMA under the conditions tested in this study (Fig. 1). In addition, DDAH activity and expression of a ddaH::lacZ reporter were not affected by a ΔPA1197 mutation (Fig. 4 and 5). These findings argue that PA1197 is not essential for DDAH activity and methylarginine utilization in P. aeruginosa PAO1. It is possible that PA1197 affects methylarginine utilization under conditions not tested in this study, including under conditions of oxygen limitation and in biofilms. For example, in the presence of NO, the catalytic cysteine residue of DDAH undergoes S-nitrosylation (34, 35), a modification that inhibits enzymatic activity. PA1197 might participate in the alleviation of this inhibition through some unknown mechanism.

MATERIALS AND METHODS

Bacteria and media.

The bacteria used in the current study are listed in Table 1. Bacteria were grown in either Lennox broth (LB) or minimal medium (22 mM KH₂PO₄, 42 mM Na₂HPO₄, 8.6 mM NaCl, 1.0 mM MgSO₄, 5.0 μM FeSO₄, pH 7.0). Minimal medium was supplemented with 15 mM carbon source and 10 mM nitrogen source as specified for each set of experiments (see below). Solid bacteriological media were prepared with the addition of Difco Bacto agar at 15 g liter⁻¹. For plasmid selection in E. coli, the media were supplemented with carbenicillin (100 μg ml⁻¹), gentamicin (20 μg ml⁻¹), or kanamycin (50 μg ml⁻¹). For plasmid and marker selection in Pseudomonas spp., the media were supplemented with carbenicillin (200 μg ml⁻¹), gentamicin (30 μg ml⁻¹), or tetracycline (25 μg ml⁻¹).

TABLE 1.

Bacteria used in the current study

Strain	Relevant characteristic(s)	Reference or source
Pseudomonas aeruginosa
PAO1	Wild type	46
PAO1 ΔddaH	ΔddaH (ΔPA1195) mutant derivative of PAO1	This study
PAO1 ΔPA1196	ΔPA1196 mutant derivative of PAO1	This study
PAO1 ΔPA1197	ΔPA1197 mutant derivative of PAO1	This study
PAO6359	rpoN::Ω-Km mutant derivative of PAO1	46
PA14	Wild type	47
PAK	Wild type	48
Pseudomonas putida KT2440	Wild type	ATCC
Pseudomonas fluorescens ATCC 13525	Wild type	ATCC
Escherichia coli TOP10	F− mcrA Δ(mrr-hsdRMS-mcrBC) ϕ80dlacZΔM15 ΔlacX74 nupG recA1 araD139 Δ(ara-leu)7697 galE15 galK16 rpsL (Strr) endA1 λ−	Invitrogen

General molecular biology procedures.

The plasmids and oligonucleotides (primers) used in the current study are listed in Table 2. The restriction endonucleases, T4 ligase, and Phusion DNA polymerase used for cloning purposes were purchased from New England BioLabs. Promega nucleic acid purification kits were used for DNA isolation. Genomic DNA from P. aeruginosa PAO1 served as the template in all PCRs.

TABLE 2.

Plasmids and oligonucleotides used in the current study^a

Plasmid or oligonucleotide	Relevant characteristics or sequence	Reference/source or purpose
Plasmids
pCR-Blunt	Cloning plasmid; Kmr	Invitrogen
pDONR221	Gateway cloning plasmid; Kmr	Invitrogen
pET15b	Expression plasmid; Cbr	EMD Millipore
pBBR1MCS-3	Broad-host-strain plasmid; Tcr	39
pBBR1MCS-5	Broad-host-strain plasmid; Gmr	39
pEX18ApGW	Gene deletion plasmid for P. aeruginosa; Cbr	36
pFLP2	Carries FLP recombinase; Cbr	49
pPS856	Carries FRT-accC1-FRT marker; Gmr	49
ΔPlac-pBBR1MCS-5	pBBR1MCS-5 minus the lac promoter; Gmr	37
pBRL631	ddaH::FRT-aacC1-FRT in pDONR221; Kmr Gmr	This study
pBRL633	PA1197::FRT-aacC1-FRT in pDONR221; Kmr Gmr	This study
pBRL635	PA1196::FRT-aacC1-FRT in pDONR221; Kmr Gmr	This study
pBRL637	ddaH::FRT-aacC1-FRT in pEX18ApGW; Cbr Gmr	This study
pBRL638	PA1197::FRT-aacC1-FRT in pEX18ApGW; Cbr Gmr	This study
pBRL639	PA1196::FRT-aacC1-FRT in pEX18ApGW; Cbr Gmr	This study
pBRL645	ddaH::lacZ in pCR-Blunt; Kmr	This study
pBRL649	ddaH::lacZ in ΔPlac-pBBR1MCS-5; Gmr	This study
pBRL671	ddaH in pCR-Blunt; Kmr	This study
pBRL672	PA1196 in pCR-Blunt; Kmr	This study
pBRL674	ddaH in pET15b; Cbr	This study
pBRL675	PA1196 in pET15b; Cbr	This study
pBRL685	ddaH in pBBR1MCS-5; Gmr	This study
pBRL686	PA1196 in pBBR1MCS-5; Gmr	This study
pBRL688	ddaH::lacZ with mutated RpoN promoter; Gmr	This study
Oligonucleotides
BL342.f	ATGACCATGATTACGGATTCACT	E. coli lacZ
BL342.r	TTATTTTTGACACCAGACCAACTGG	E. coli lacZ
BL579.f	TACAAAAAAGCAGGCTCGAACGCATCCTGGTCATCAC	PA1197 UpF-GWL
BL579.r	TCAGAGCGCTTTTGAAGCTAATTCGTGCTTCTGCAACTCGGCGATG	PA1197 UpR-Gm
BL580.f	AGGAACTTCAAGATCCCCAATTCGGTACCGCGAATTGCGCAAAG	PA1197 DnF-Gm
BL580.r	TACAAGAAAGCTGGGTCGATAAATGTGACTTACCACCTG	PA1197 DnR-GWR
BL581.f	GGCCTGCAGCGTATCGATC	ddaH::lacZ
BL581.r	GAATCCGTAATCATGGTCATGACGATTTTCCTCGTGTGG	ddaH::lacZ
BL587.f	TACAAAAAAGCAGGCTCGCTTCGCGTGGAAATCGTC	ddaH UpF-GWL
BL587.r	TCAGAGCGCTTTTGAAGCTAATTCGCGAGCGATGATGTGCTTGAAC	ddaH UpR-Gm
BL588.f	AGGAACTTCAAGATCCCCAATTCGGTCAACGAAAGGGTGATCATGC	ddaH DnF-Gm
BL588.r	TACAAGAAAGCTGGGTCAGTTTTCCCTTGTCCGAATCG	ddaH DnR-GWR
BL614.f	GCCATATGTTCAAGCACATCATCGCTC	ddaH ORF
BL614.r	GCGGATCCGAGCTCTCAGAAGCGCAGCGACATGC	ddaH ORF
BL615.f	GCCATATGGCGCTTGTCGAGGAACC	PA1196 ORF
BL615.r	GCGGATCCGAGCTCTCAGGCTGGCGGATCGAG	PA1196 ORF
BL618.f	GGCGTTGGCTAACGCGTGGCTT	Mutagenesis of pBRL649
BL618.r	CGGGAATTGCCTTGGAAATCC	Mutagenesis of pBRL649
ZS412.f	TACAAAAAAGCAGGCTATGGCGCTTGTCGAGGAAC	PA1196 UpF-GWL
ZS412.r	TCAGAGCGCTTTTGAAGCTAATTCGGGCCCCCACGTAGGCCTG	PA1196 UpR-Gm
ZS413.f	AGGAACTTCAAGATCCCCAATTCGGTGATCCGGCGCAGCCTGTTGCTGC	PA1196 DnF-Gm
ZS413.r	TACAAGAAAGCTGGGTTCAGGCTGGCGGATCGAG	PA1196 DnR-GWR
Gm-F	CGAATTAGCTTCAAAAGCGCTCTGA	FRT-aacC1-FRT marker
Gm-R	CGAATTGGGGATCTTGAAGTTCCT	FRT-aacC1-FRT marker
GW-attB1	GGGGACAAGTTTGTACAAAAAAGCAGGCT	Gateway cloning primer
GW-attB2	GGGGACCACTTTGTACAAGAAAGCTGGGT	Gateway cloning primer

^aPlasmids carry the bla, aacC1, aph(3′)-II, and/or tetC gene encoding resistance to carbenicillin (Cb^r), gentamicin (Gm^r), kanamycin (Km^r), and/or tetracycline (Tc^r), respectively. FRT, FLP recombination target. The following abbreviations referring to the target and purpose of gene deletion primers correspond to the gene deletion strategy for P. aeruginosa (49): UpF, up forward; UpR, up reverse; DnF, down forward; DnR, down reverse; GWL, Gateway left; GWR, Gateway right; and Gm, gentamicin marker.

Deletion of the PA1195 (ddaH), PA1196, and PA1197 genes in P. aeruginosa PAO1.

The PA1195 (ddaH), PA1196, and PA1197 genes were deleted from P. aeruginosa PAO1 using well-established procedures (36–38). The primers and plasmids pertaining to the gene deletions are given in Table 2.

Cloning of the PA1195 (ddaH) and PA1196 genes.

The ddaH and PA1196 ORFs were PCR amplified from the genomic DNA of P. aeruginosa PAO1 using primer pairs BL614.f/BL614.r and BL615.f/BL615.r, respectively. The desired ddaH and PA1196 PCR products were gel purified and cloned into pCR-Blunt (Invitrogen) to generate the plasmids pBRL671 and pBRL672, respectively. To install a 5′ ribosome-binding site (RBS), the ddaH and PA1196 ORFs were subcloned into the NdeI/BamHI sites of pET15b (EMD Millipore) to generate the plasmids pBRL674 and pBRL675, respectively. The RBS-ddaH and RBS-PA1196 fragments were then each subcloned into the XbaI/SacI sites of the expression plasmid pBBR1MCS-5 (39) to give plasmids pBRL685 and pBRL686, respectively. Lastly, the PA1196 ORF from pBRL672 was subcloned into the XbaI site of pBBR1MCS-3 (39) with either a backward (pBRL719) or a forward (pBRL720) orientation relative to the orientation of the lac promoter.

Cloning of the ddaH::lacZ reporter.

The ddaH::lacZ reporter was constructed through fusion PCR (40). Briefly, the primers BL581.f and BL581.r were used to PCR amplify the 5′ regulatory region (∼500 bp) of the ddaH gene. The primers BL342.f and BL342.r were used to PCR amplify the E. coli lacZ ORF (∼3000 bp). The ddaH and lacZ amplicons were next fused together in a PCR with the primers BL581.f and BL342.r. The desired ddaH::lacZ fusion was gel purified and cloned into pCR-Blunt (Invitrogen) to generate pBRL645. The ddaH::lacZ fusion was subcloned into the XbaI site of ΔPlac-pBBR1MCS-5 (37) to give pBRL649. In addition, Q5 site-directed mutagenesis (NEB) was performed using primers BL618.f and BL618.r to change the GG nucleotides of the −24 element of the RpoN promoter to AA in ddaH::lacZ of pBRL649. The resulting plasmid, pBRL688, was sequenced to verify the presence of the desired mutation.

Growth assays.

ADMA hydrochloride and l-NMMA acetate were purchased from Sigma-Aldrich. However, due to the presence of acetate in the l-NMMA preparation, this methylarginine was excluded from the growth assays. Furthermore, for the experiments to be cost-effective, growth was assayed using a microplate reader. Growth was measured in quadruplicate for each P. aeruginosa strain. Bacteria were initially grown on LB agar plates at 37°C for 24 h. Single colonies were inoculated into 2 ml of LB (in a 16- by 100-mm culture tube), and the inoculated or seed cultures were grown at 37°C at 200 rpm for 24 h. The wells of 96-well polystyrene plates were filled with 0.2 ml of minimal medium supplemented with 15 mM gluconate and 10 mM nitrogen source (ADMA, l-arginine, l-citrulline, dimethylamine, l-ornithine, or NH₄Cl). The minimal medium-filled wells were inoculated with 1% (vol/vol) LB-grown seed culture. The inoculated plates were incubated at 37°C with continuous slow shaking in a Synergy HT BioTek microplate reader. The absorbance at 600 nm (OD₆₀₀) of each well was measured at 1.0-h intervals for a total duration of 24 to 48 h.

Exceptions to this procedure included the following: (i) when ADMA was tested as a carbon source, the minimal media were supplemented with 15 mM ADMA and 10 mM NH₄Cl, (ii) for complementation experiments, the media were supplemented 30 μg ml⁻¹ gentamicin for plasmid selection, and (iii) a temperature of 30°C (instead of 37°C) was used when the growth of various Pseudomonas spp. on ADMA as a nitrogen source was tested.

β-Galactosidase (LacZ) assays.

LacZ activities were measured using the Miller assay (40, 41), and experiments were conducted in triplicate for each strain and/or condition. The ddaH::lacZ reporter (pBRL649) was electroporated into P. aeruginosa, and colonies were selected on LB agar plates supplemented with 30 μg ml⁻¹ gentamicin. Individual colonies were inoculated into 2 ml of LB (in a 16- by 100-mm culture tube) supplemented with 30 μg ml⁻¹ gentamicin, and the inoculated or seed cultures were grown at 37°C at 200 rpm for 24 h. Minimal medium (1 ml in a 16- by 100-mm culture tube) supplemented with 15 mM gluconate, 10 mM NH₄Cl, and 30 μg ml⁻¹ gentamicin was inoculated with 1% (vol/vol) LB-grown seed culture, and the inoculated cultures were grown at 37°C at 200 rpm. At an OD₆₀₀ of 0.3, cultures were treated with a final concentration of 0.1 mM substrate, which included ADMA, l-NMMA, l-citrulline, or l-arginine. LacZ activities were measured at 1.0 h afer the addition of the substrate. Analysis of variance (ANOVA) was done using Dunnett's post hoc test (α value, 0.05) to identify significant differences (P < 0.0001) in LacZ activities.

P. putida KT2440 was cotransformed with the ddaH::lacZ reporter (pBRL649) and plasmid-derived PA1196 (pBRL720) via electroporation (42). Recombinant colonies were selected on LB supplemented with 30 μg ml⁻¹ gentamicin and 25 μg ml⁻¹ tetracycline. Individual colonies were inoculated into 2 ml of LB (in a 16- by 100-mm culture tube) supplemented with 30 μg ml⁻¹ gentamicin and 25 μg ml⁻¹ tetracycline, and the inoculated or seed cultures were grown at 30°C at 200 rpm for 24 h. Minimal medium (1 ml in a 16- by 100-mm culture tube) supplemented with 15 mM gluconate, 10 mM NH₄Cl, 30 μg ml⁻¹ gentamicin, and 25 μg ml⁻¹ tetracycline was inoculated with 2% (vol/vol) LB-grown seed culture, and the inoculated cultures were grown at 30°C at 200 rpm. At an OD₆₀₀ of 0.3, the cultures were treated with either no substrate or 0.1 mM ADMA. LacZ activities were measured at 2.0 h after the addition of the substrate. LacZ assays (controls) were also performed with P. putida KT2440 cotransformed with empty plasmids pBBR1MCS-3/ΔPlac-pBBR1MCS-5, pBBR1MCS-3/pBRL649, pBRL720/ΔPlac-pBBR1MCS-5, and pBRL719/pBRL649. ANOVA was done using Dunnett's post hoc test (α value, 0.05) to identify significant differences (P < 0.0001) in LacZ activities.

Measurement of DDAH activity.

DDAH activity was measured in duplicate for each P. aeruginosa strain per tested condition. Bacteria were initially grown on LB agar plates at 37°C for 24 h. Single colonies were used to inoculate 2 ml of LB (in a 16- by 100-mm culture tube), and the inoculated or seed cultures were grown at 37°C at 200 rpm for 24 h. Minimal medium (5 ml in a 50-ml conical centrifuge tube) supplemented with 15 mM gluconate and 10 NH₄Cl was inoculated with 1% (vol/vol) LB-grown seed culture. The inoculated cultures were grown at 37°C at 200 rpm to an OD₆₀₀ of 0.3 and subsequently treated with either no substrate or 1.0 mM ADMA. At 2.0 h after the addition of the substrate, bacteria were harvested via centrifugation. Extracts were prepared from the cells as previously described (43). Briefly, cells were lysed by sonication on ice, debris and unlysed cells were removed by centrifugation, and the cell-free supernatants were washed and concentrated in a Microcon centrifugal filter (Millipore). The protein content of cell extracts was quantified using the Bradford assay (Pierce). The DDAH activity in the cell extracts was measured using established procedures (44, 45) and is reported in units (U), defined as the amount of l-citrulline (nanomoles hour⁻¹) formed per milligram of total protein. ANOVA was done using Dunnett's post hoc test (α value, 0.05) to identify significant differences (P < 0.0001) in DDAH activities.